Unity just recently added full 2d support:
When I choose rph_"Build and Run" under Windows Store Apps I can select "D3D11 C++ solution" and get a full solution file that I can pull up and edit in VS 2013, haven't looked at it closely though, could be a completely garbled mess...
Hmmm, the 2d support doesn't mean that they remove the overhead from the 3d side of things, rather it at the moment is kind of a tacked on thing. It may get better eventually, but for 2d, GMStudio is still much better if you don't need the 3d stuff.
About the C++ project, that is news to me. My question then would be though, how much of the engine gets output to that C++ project? I would assume you don't have any access to the internals to the Unity Engine itself, rather they would be gettin gcalled externally though precompiled files(like DLLS). Also, Unity sells a separate source license to the engine, so it wouldn't make much sense to allow the source to so easily be used.
I think that the purpose of this C++ project is to allow you to compile the game, but probably not for modifying afterwards, rather just to compile. It may be that instead of trying to call the compiler etc... themselves, they spit out a project and make you compile it. That doesn't mean that the project is very easily modifiable. For example, the normal exports spit out a "runner" executable, and every class(script, etc...) gets put into a "Mono DLL" of sorts. It may be something similar happening here. On the other hand, I could be completely wrong.
In any case, I would also think that by using the C++ to finish the project(as in not just compile, but actually program) the game would be a waste. The point of using Unity for many people is the ease of development, for a single platform, and moreso for multiple platforms. By editing the C++ project(assuming I'm wrong about the above paragraph), you are losing that benefit. Also, you wouldn't be able to use those changes on other platforms later if you wished to port. Unity(and GMStudio) make things so easy to port to different platforms, that you really wouldn't want to lose that, even if you don't plan on using the other exports now, as you never know how successful your game could be.