SCons has served its purpose, but it is increasingly not a great fit for the way MyPaint works. SCons is weird and nonstandard, and people hate it. In particular, SCons is horrid for CI environments like MSYS2 on AppVeyor. It tries to be a little too clever in those circumstances, and tries to use toolchains outside the install tree. Hilarity ensues.
This will help support the Python 3 porting project, since SCons is pretty new to that territory. Pip is the standard, and we should adopt the standard tools for Python development.