I've been using WinKawaks for my CPS I, II, and Neo-Geo games, while running all three (plus others; i'll explain in a bit) through GameEx, my front end. I posted a thread in here a few days ago asking which version of MAME to use when running MK II, III, and UMK III. HarumaN told me that he was using version 0.78, so I decided to use that version to see how my MAME games played in that version vs 0.136 - which I have also had problems with running The Simpsons, TMNT, etc. 0.78 runs all of my MKs flawlessly, but it's crippled other games in various ways, e.g., Donkey Kong has random sounds that generate out of nowhere and his "squeak" when he walks is completely missing. So, what I did was set up GameEx to run 3 versions of WinKawaks - one for each set of games, CPS I, II and Neo-Geo, then created 2 separate entries for MAME - one for 0.78 and one for 0.135, which seemed to run most of what I wanted aside from the MKs, and took care of the bad ROM issue. In addition, I also have it set to run my NES, SNES, Genesis, Sega CD, etc. ROMs through the frontend, so it's completely seamless.
My point is, is that you might want to consider using your frontend to run different versions of MAME to suit your needs. Just create separate directories per version, and place the roms that work the best into each of those directories. Just a thought.