diff --git a/src/deprecations.jl b/src/deprecations.jl
index 73df50ecc4..aaafa0d283 100644
--- a/src/deprecations.jl
+++ b/src/deprecations.jl
@@ -8,3 +8,165 @@ macro mtkbuild(exprs...)
         @mtkcompile $(exprs...)
     end |> esc
 end
+
+for T in [:ODESystem, :NonlinearSystem, :DiscreteSystem, :ImplicitDiscreteSystem]
+    @eval @deprecate $T(args...; kwargs...) System(args...; kwargs...)
+end
+
+for T in [:ODEProblem, :DDEProblem, :SDEProblem, :SDDEProblem, :DAEProblem,
+    :BVProblem, :DiscreteProblem, :ImplicitDiscreteProblem]
+    for (pType, pCanonical) in [
+            (AbstractDict, :p),
+            (AbstractArray{<:Pair}, :(Dict(p))),
+            (AbstractArray, :(isempty(p) ? Dict() : Dict(parameters(sys) .=> p)))
+        ],
+        (uType, uCanonical) in [
+            (Nothing, :(Dict())),
+            (AbstractDict, :u0),
+            (AbstractArray{<:Pair}, :(Dict(u0))),
+            (AbstractArray, :(isempty(u0) ? Dict() : Dict(unknowns(sys) .=> u0)))
+        ]
+
+        @eval function SciMLBase.$T(sys::System, u0::$uType, tspan, p::$pType; kw...)
+            ctor = string($T)
+            uCan = string($(QuoteNode(uCanonical)))
+            pCan = string($(QuoteNode(pCanonical)))
+            @warn """
+            `$ctor(sys, u0, tspan, p; kw...)` is deprecated. Use
+            `$ctor(sys, merge($uCan, $pCan), tspan)` instead.
+            """
+            SciMLBase.$T(sys, merge($uCanonical, $pCanonical), tspan; kw...)
+        end
+        @eval function SciMLBase.$T{iip}(
+                sys::System, u0::$uType, tspan, p::$pType; kw...) where {iip}
+            ctor = string($T{iip})
+            uCan = string($(QuoteNode(uCanonical)))
+            pCan = string($(QuoteNode(pCanonical)))
+            @warn """
+            `$ctor(sys, u0, tspan, p; kw...)` is deprecated. Use
+            `$ctor(sys, merge($uCan, $pCan), tspan)` instead.
+            """
+            return SciMLBase.$T{iip}(sys, merge($uCanonical, $pCanonical), tspan; kw...)
+        end
+        @eval function SciMLBase.$T{iip, spec}(
+                sys::System, u0::$uType, tspan, p::$pType; kw...) where {iip, spec}
+            ctor = string($T{iip, spec})
+            uCan = string($(QuoteNode(uCanonical)))
+            pCan = string($(QuoteNode(pCanonical)))
+            @warn """
+            `$ctor(sys, u0, tspan, p; kw...)` is deprecated. Use
+            `$ctor(sys, merge($uCan, $pCan), tspan)` instead.
+            """
+            return $T{iip, spec}(sys, merge($uCanonical, $pCanonical), tspan; kw...)
+        end
+    end
+
+    for pType in [SciMLBase.NullParameters, Nothing], uType in [Any, Nothing]
+        @eval function SciMLBase.$T(sys::System, u0::$uType, tspan, p::$pType; kw...)
+            ctor = string($T)
+            pT = string($(QuoteNode(pType)))
+            @warn """
+            `$ctor(sys, u0, tspan, p::$pT; kw...)` is deprecated. Use
+            `$ctor(sys, u0, tspan)` instead.
+            """
+            $T(sys, u0, tspan; kw...)
+        end
+        @eval function SciMLBase.$T{iip}(
+                sys::System, u0::$uType, tspan, p::$pType; kw...) where {iip}
+            ctor = string($T{iip})
+            pT = string($(QuoteNode(pType)))
+            @warn """
+            `$ctor(sys, u0, tspan, p::$pT; kw...)` is deprecated. Use
+            `$ctor(sys, u0, tspan)` instead.
+            """
+            return $T{iip}(sys, u0, tspan; kw...)
+        end
+        @eval function SciMLBase.$T{iip, spec}(
+                sys::System, u0::$uType, tspan, p::$pType; kw...) where {iip, spec}
+            ctor = string($T{iip, spec})
+            pT = string($(QuoteNode(pType)))
+            @warn """
+            `$ctor(sys, u0, tspan, p::$pT; kw...)` is deprecated. Use
+            `$ctor(sys, u0, tspan)` instead.
+            """
+            return $T{iip, spec}(sys, u0, tspan; kw...)
+        end
+    end
+end
+
+for T in [:NonlinearProblem, :NonlinearLeastSquaresProblem,
+    :SCCNonlinearProblem, :OptimizationProblem, :SteadyStateProblem]
+    for (pType, pCanonical) in [
+            (AbstractDict, :p),
+            (AbstractArray{<:Pair}, :(Dict(p))),
+            (AbstractArray, :(isempty(p) ? Dict() : Dict(parameters(sys) .=> p)))
+        ],
+        (uType, uCanonical) in [
+            (Nothing, :(Dict())),
+            (AbstractDict, :u0),
+            (AbstractArray{<:Pair}, :(Dict(u0))),
+            (AbstractArray, :(isempty(u0) ? Dict() : Dict(unknowns(sys) .=> u0)))
+        ]
+
+        @eval function SciMLBase.$T(sys::System, u0::$uType, p::$pType; kw...)
+            ctor = string($T)
+            uCan = string($(QuoteNode(uCanonical)))
+            pCan = string($(QuoteNode(pCanonical)))
+            @warn """
+            `$ctor(sys, u0, p; kw...)` is deprecated. Use `$ctor(sys, merge($uCan, $pCan))`
+            instead.
+            """
+            $T(sys, merge($uCanonical, $pCanonical); kw...)
+        end
+        @eval function SciMLBase.$T{iip}(
+                sys::System, u0::$uType, p::$pType; kw...) where {iip}
+            ctor = string($T{iip})
+            uCan = string($(QuoteNode(uCanonical)))
+            pCan = string($(QuoteNode(pCanonical)))
+            @warn """
+            `$ctor(sys, u0, p; kw...)` is deprecated. Use `$ctor(sys, merge($uCan, $pCan))`
+            instead.
+            """
+            return $T{iip}(sys, merge($uCanonical, $pCanonical); kw...)
+        end
+        @eval function SciMLBase.$T{iip, spec}(
+                sys::System, u0::$uType, p::$pType; kw...) where {iip, spec}
+            ctor = string($T{iip, spec})
+            uCan = string($(QuoteNode(uCanonical)))
+            pCan = string($(QuoteNode(pCanonical)))
+            @warn """
+            `$ctor(sys, u0, p; kw...)` is deprecated. Use `$ctor(sys, merge($uCan, $pCan))`
+            instead.
+            """
+            return $T{iip, spec}(sys, merge($uCanonical, $pCanonical); kw...)
+        end
+    end
+    for pType in [SciMLBase.NullParameters, Nothing], uType in [Any, Nothing]
+        @eval function SciMLBase.$T(sys::System, u0::$uType, p::$pType; kw...)
+            ctor = string($T)
+            pT = string($(QuoteNode(pType)))
+            @warn """
+            `$ctor(sys, u0, p::$pT; kw...)` is deprecated. Use `$ctor(sys, u0)` instead
+            """
+            $T(sys, u0; kw...)
+        end
+        @eval function SciMLBase.$T{iip}(
+                sys::System, u0::$uType, p::$pType; kw...) where {iip}
+            ctor = string($T{iip})
+            pT = string($(QuoteNode(pType)))
+            @warn """
+            `$ctor(sys, u0, p::$pT; kw...)` is deprecated. Use `$ctor(sys, u0)` instead
+            """
+            return $T{iip}(sys, u0; kw...)
+        end
+        @eval function SciMLBase.$T{iip, spec}(
+                sys::System, u0::$uType, p::$pType; kw...) where {iip, spec}
+            ctor = string($T{iip, spec})
+            pT = string($(QuoteNode(pType)))
+            @warn """
+            `$ctor(sys, u0, p::$pT; kw...)` is deprecated. Use `$ctor(sys, u0)` instead
+            """
+            return $T{iip, spec}(sys, u0; kw...)
+        end
+    end
+end
diff --git a/src/discretedomain.jl b/src/discretedomain.jl
index f8a1a17009..73e6b8b7fa 100644
--- a/src/discretedomain.jl
+++ b/src/discretedomain.jl
@@ -231,7 +231,7 @@ function (xn::Num)(k::ShiftIndex)
     @unpack clock, steps = k
     x = value(xn)
     # Verify that the independent variables of k and x match and that the expression doesn't have multiple variables
-    vars = Symbolics.get_variables(x)
+    vars = ModelingToolkit.vars(x)
     if length(vars) != 1
         error("Cannot shift a multivariate expression $x. Either create a new unknown and shift this, or shift the individual variables in the expression.")
     end
diff --git a/src/problems/bvproblem.jl b/src/problems/bvproblem.jl
index 7040b32ffd..6344dfaa0b 100644
--- a/src/problems/bvproblem.jl
+++ b/src/problems/bvproblem.jl
@@ -8,6 +8,8 @@
     check_compatibility && check_compatible_system(BVProblem, sys)
     isnothing(callback) || error("BVP solvers do not support callbacks.")
 
+    dvs = unknowns(sys)
+    op = to_varmap(op, dvs)
     # Systems without algebraic equations should use both fixed values + guesses
     # for initialization.
     _op = has_alg_eqs(sys) ? op : merge(Dict(op), Dict(guesses))
@@ -17,7 +19,6 @@
         t = tspan !== nothing ? tspan[1] : tspan, check_compatibility = false, cse,
         checkbounds, time_dependent_init = false, expression, kwargs...)
 
-    dvs = unknowns(sys)
     stidxmap = Dict([v => i for (i, v) in enumerate(dvs)])
     u0_idxs = has_alg_eqs(sys) ? collect(1:length(dvs)) :
               [stidxmap[k] for (k, v) in op if haskey(stidxmap, k)]
diff --git a/src/systems/nonlinear/initializesystem.jl b/src/systems/nonlinear/initializesystem.jl
index 7769f20837..beb2719c2c 100644
--- a/src/systems/nonlinear/initializesystem.jl
+++ b/src/systems/nonlinear/initializesystem.jl
@@ -167,7 +167,7 @@ function generate_initializesystem_timevarying(sys::AbstractSystem;
     for k in keys(defs)
         defs[k] = substitute(defs[k], paramsubs)
     end
-    isys = System(eqs_ics,
+    isys = System(Vector{Equation}(eqs_ics),
         vars,
         pars;
         defaults = defs,
@@ -280,7 +280,7 @@ function generate_initializesystem_timeindependent(sys::AbstractSystem;
     for k in keys(defs)
         defs[k] = substitute(defs[k], paramsubs)
     end
-    isys = System(eqs_ics,
+    isys = System(Vector{Equation}(eqs_ics),
         vars,
         pars;
         defaults = defs,
diff --git a/src/systems/system.jl b/src/systems/system.jl
index 1b0fa940f6..5c01557cb5 100644
--- a/src/systems/system.jl
+++ b/src/systems/system.jl
@@ -543,12 +543,11 @@ function System(eqs::Vector{Equation}; kwargs...)
     for ssys in get(kwargs, :systems, System[])
         collect_scoped_vars!(allunknowns, ps, ssys, nothing)
     end
-    costs = get(kwargs, :costs, nothing)
-    if costs !== nothing
-        costunknowns, costps = process_costs(costs, allunknowns, ps, nothing)
-        union!(allunknowns, costunknowns)
-        union!(ps, costps)
+    costs = get(kwargs, :costs, [])
+    for val in costs
+        collect_vars!(allunknowns, ps, val, nothing)
     end
+
     cstrs = Vector{Union{Equation, Inequality}}(get(kwargs, :constraints, []))
     for eq in cstrs
         collect_vars!(allunknowns, ps, eq, nothing)
diff --git a/test/sciml_problem_inputs.jl b/test/sciml_problem_inputs.jl
index c02bd9dea1..cd081118fb 100644
--- a/test/sciml_problem_inputs.jl
+++ b/test/sciml_problem_inputs.jl
@@ -2,7 +2,7 @@
 
 # Fetch packages
 using ModelingToolkit, JumpProcesses, NonlinearSolve, OrdinaryDiffEq, StaticArrays,
-      SteadyStateDiffEq, StochasticDiffEq, Test
+      SteadyStateDiffEq, StochasticDiffEq, SciMLBase, Test
 using ModelingToolkit: t_nounits as t, D_nounits as D
 
 # Sets rnd number.
@@ -101,7 +101,7 @@ begin
 end
 
 # Perform ODE simulations (singular and ensemble).
-let
+@testset "ODE" begin
     # Creates normal and ensemble problems.
     base_oprob = ODEProblem(osys, [u0_alts[1]; p_alts[1]], tspan)
     base_sol = solve(base_oprob, Tsit5(); saveat = 1.0)
@@ -119,7 +119,7 @@ let
 end
 
 # Solves a nonlinear problem (EnsembleProblems are not possible for these).
-let
+@testset "Nonlinear" begin
     base_nlprob = NonlinearProblem(nsys, [u0_alts[1]; p_alts[1]])
     base_sol = solve(base_nlprob, NewtonRaphson())
     # Solves problems for all input types, checking that identical solutions are found.
@@ -130,7 +130,7 @@ let
 end
 
 # Perform steady state simulations (singular and ensemble).
-let
+@testset "SteadyState" begin
     # Creates normal and ensemble problems.
     base_ssprob = SteadyStateProblem(osys, [u0_alts[1]; p_alts[1]])
     base_sol = solve(base_ssprob, DynamicSS(Tsit5()))
@@ -146,3 +146,85 @@ let
         @test base_esol == solve(eprob, DynamicSS(Tsit5()); trajectories = 2)
     end
 end
+
+@testset "Deprecations" begin
+    @variables _x(..) = 1.0
+    @parameters p = 1.0
+    @brownian a
+    x = _x(t)
+    k = ShiftIndex(t)
+
+    @test_deprecated ODESystem([D(x) ~ x * p], t; name = :a)
+    @mtkcompile odesys = System([D(x) ~ x * p], t)
+    @mtkcompile sdesys = System([D(x) ~ x * p + a], t)
+    @test_deprecated NonlinearSystem([0 ~ x^3 + p]; name = :a)
+    @mtkcompile nlsys = System([0 ~ x^3 + p])
+    @mtkcompile ddesys = System([D(x) ~ x * p + _x(t - 0.1)], t)
+    @mtkcompile sddesys = System([D(x) ~ x * p + _x(t - 0.1) + a], t)
+    @test_deprecated DiscreteSystem([x ~ x(k - 1) + x(k - 2)], t; name = :a)
+    @mtkcompile discsys = System([x ~ x(k - 1) * p], t)
+    @test_deprecated ImplicitDiscreteSystem([x ~ x(k - 1) + x(k - 2) * p * x], t; name = :a)
+    @mtkcompile idiscsys = System([x ~ x(k - 1) * p * x], t)
+    @mtkcompile optsys = OptimizationSystem(x^2 + p)
+
+    u0s = [
+        Dict(x => 1.0),
+        [x => 1.0],
+        [1.0],
+        [],
+        nothing
+    ]
+    ps = [
+        Dict(p => 1.0),
+        [p => 1.0],
+        [1.0],
+        [],
+        nothing,
+        SciMLBase.NullParameters()
+    ]
+    tspan = (0.0, 1.0)
+
+    @testset "$ctor" for (sys, ctor) in [
+        (odesys, ODEProblem),
+        (odesys, ODEProblem{true}),
+        (odesys, ODEProblem{true, SciMLBase.FullSpecialize}), (odesys, BVProblem),
+        (odesys, BVProblem{true}),
+        (odesys, BVProblem{true, SciMLBase.FullSpecialize}), (sdesys, SDEProblem),
+        (sdesys, SDEProblem{true}),
+        (sdesys, SDEProblem{true, SciMLBase.FullSpecialize}), (ddesys, DDEProblem),
+        (ddesys, DDEProblem{true}),
+        (ddesys, DDEProblem{true, SciMLBase.FullSpecialize}), (sddesys, SDDEProblem),
+        (sddesys, SDDEProblem{true}),
+        (sddesys, SDDEProblem{true, SciMLBase.FullSpecialize}),
+
+        # (discsys, DiscreteProblem),
+        # (discsys, DiscreteProblem{true}),
+        # (discsys, DiscreteProblem{true, SciMLBase.FullSpecialize}),
+
+        (idiscsys, ImplicitDiscreteProblem),
+        (idiscsys, ImplicitDiscreteProblem{true}),
+        (idiscsys, ImplicitDiscreteProblem{true, SciMLBase.FullSpecialize})
+    ]
+        @testset "$(typeof(u0)) - $(typeof(p))" for u0 in u0s, p in ps
+            if u0 isa Vector{Float64} && ctor <: ImplicitDiscreteProblem
+                u0 = ones(2)
+            end
+            @test_warn ["deprecated"] ctor(sys, u0, tspan, p)
+        end
+    end
+    @testset "$ctor" for (sys, ctor) in [
+        (nlsys, NonlinearProblem),
+        (nlsys, NonlinearProblem{true}),
+        (nlsys, NonlinearProblem{true, SciMLBase.FullSpecialize}), (
+            nlsys, NonlinearLeastSquaresProblem),
+        (nlsys, NonlinearLeastSquaresProblem{true}),
+        (nlsys, NonlinearLeastSquaresProblem{true, SciMLBase.FullSpecialize}), (
+            nlsys, SCCNonlinearProblem),
+        (nlsys, SCCNonlinearProblem{true}), (optsys, OptimizationProblem),
+        (optsys, OptimizationProblem{true})
+    ]
+        @testset "$(typeof(u0)) - $(typeof(p))" for u0 in u0s, p in ps
+            @test_warn ["deprecated"] ctor(sys, u0, p)
+        end
+    end
+end