If microsoft did make windows run linux apps it would be done with another subsystem, you have probably run an app on a subsystem other than the native win32 and surely didn't notice a speed difference. It's only a small layer in between so it's menial compared to the time it takes to do large drawing loops, sorting, etc.
Here are the subsystems in nt:
DOS Virtual Machine
Also, WINE is plenty fast for your general windows app, it's not an emulator.
I may have just misinterpreted what you said but it sounded like you think the windows PE format has different binary than that of ELF, binary only changes across cpu hardware architecture. Making windows execute ELF and linux execute PE would be quite easy, it's the function/system calls that are problematic.
Finally, making all linux apps run on windows won't refine or improve the actual microkernel or executive.