Yes the stability issue from build-to-build has been a problem for a while, but that now that you have got rid of the zpu and firmware at least some improvement must have been made. Also with a larger fpga routing should have a higher chance to succeed, but as I have learned setting up proper constraints should really be the key to a proper routing from build-to-build. Since many of us seem to have a software background (including myself) this is something new to learn. We did make a shortcut, to set routing option for low power optimization, which would shorten the signal path, but it also increases the routing processing time a little bit. Note that the Genesis is actually a quite complex system, having two different computers (68k and z80) communicating over a shared bus, dma etc. It is actally not that far from SEGAs system 16 arcade board, only with a weaker video display sub-system.
The core has been inherited from Torlus, so I am not aware of all features. I have started several attempts to clean it up, for example I wanted to lift out the scandoubler from the vdp and use the external scandoubler used by many MiST projects but failed. Maybe it has to do with the fact that a scanline is 3420/80 = 427,5 pixels clocks, and the scandoubler module can't handle that.
@Sorgelig, great progress with fixing the sprite flickering issue! I never realized that an fpga could have so much memory to fit the video ram for a 16-bit system. Strage with reverse Sonic, are you sure you are not using a hacked rom? What about other platformers, are they reversed too?