Problem

MonoDevelop's Build System is not future save.
it contains a lot of workarounds of old .net-versions, and code from that time when MSBuild was closed source
at least it's broken already if .net5 is installed.

current implementation uses some hacky tricks to work around, see:

affected projects:
https://github.com/dotdevelop/dotdevelop/tree/master/main/src/core/MonoDevelop.Core/MonoDevelop.Projects.MSBuild
https://github.com/dotdevelop/dotdevelop/tree/master/main/src/core/MonoDevelop.Projects.Formats.MSBuild

and for NuGet:
https://github.com/dotdevelop/dotdevelop/tree/master/main/src/addins/MonoDevelop.PackageManagement

possible solution

there is a lot of similar code around, actively supported
but most of it not public accesible (internal, private etc.)

clone this repos, branch it & make usable code accessible (eg. internal visible to, wrapper project) or adopt it

MSBuild:

https://github.com/dotdevelop/msbuild (partly cloned in https://github.com/dotdevelop/dotdevelop/tree/master/main/src/core/MonoDevelop.Core/MonoDevelop.Projects.MSBuild)

Mono-MsBuild
https://github.com/mono/msbuild/commits/mono-2019-12

and also similar problems are solved in OmniSharp:
https://github.com/dotdevelop/omnisharp-roslyn/tree/master/src/OmniSharp.MSBuild

see also: https://github.com/OmniSharp/csharp-language-server-protocol

NuGet:

https://github.com/NuGet/NuGet.Client
https://github.com/NuGet/NuGet.Client/tree/dev/src/NuGet.Clients/NuGet.PackageManagement.UI (partly cloned in https://github.com/dotdevelop/dotdevelop/tree/master/main/src/addins/MonoDevelop.PackageManagement)

etc. see NuGet.VisualStudio ff

deliver own versions

there should be local, proved working fallback versions packaged with MonoDevelop to avoid problems with wild MS updates, as shown in the past.

minimum 2 msbuild fallback versions:

one for dotnetcore (building 2.1,3.1,5 ff)

one for .net framework, a mono framework version at least is in https://github.com/dotnet/msbuild/blob/vs16.9 if FullFrameworkTFM or MonoBuild is set.

Package a recent nuget.exe used by monodevelop.

there is no reason why there should be a lot of workarounds for old versions to avoid some mb of extra data.