I think you'll find that the hard drive games are still far from perfect, even in the latest releases of MAME.
Due to the higher level of technology in those machines, I don't think emulation will ever do the trick as most 3D games feature dedicated graphics and sound engines which are still not sussed out. It's just like Killer Instinct - Still nowhere near at the level I enjoy, so I prefer to play it using the U64 emulator which does it so much better, but still has a few bugs.
I know there is no other emulator for these games, but I think it's still relatively early days and until MAME includes coding borrowed from outside projects I don't think the progress will be as rapid as it was for the oldies that were cracked in their dozens.
Plus, here's a thought - run everything through DOS or Windows 98 at the very least. XP is just crap.