With all the different configurations of hardware that MAME is emulating, it’s never going to be 100% compatible for everything. Not everything has been documented well and there may be last-minute customizations/details the original hardware manufacturers left off the spec sheets/manuals for some arcade machines. MAME’s also developed as a side project/hobby by many different people. Some may or may not have connections with the arcade industry; it’s still a hobby project and an evolving one.
MAME really doesn’t take up that much disk space so having more than 1 version on-HD to play specific titles shouldn’t be an issue. There are always games that won’t run in the latest version or have issues that keep them from being 100%. I can’t be specific about ROM titles or provide links because of the rules… It’s a big no-no to link/discuss games that may still be under copyright protection and, of course, SRK’s tie-in corporations/cash/prize providers don’t look kindly on the emulation scene, either.
There are still tons of earlier games that don’t work well on any emulator out there. I think personally that the 16-bit era is covered fairly well and understood by the emulation scene. 8-bit? Well, there are probably more problems there because of the distance time-wise between today and when many of those games were released. Most of the early games are just not that popular and failed to become iconic industry standards. There are just far more (still) active videogame players from the 16-bit era. People 10-years-and-older than me generally don’t play the latest videogames anymore. There were some pretty exotic pieces of customized hardware used during the 8-bit era – some of it for only one game or a short series; some of it proprietary and confidential – and not all of it is understood. Also, unless your game is part of Atari’s classics, the Pac-Man series, or Donkey Kong games, chances are that the game has never been emulated well since the original arcade release.
The moneymaking games always come back in one form or another, sometimes with the original arcade code emulated properly. The other stuff, especially if it’s based on a licensed brand like a motion picture or TV series, not so much. There’s no incentive for companies to re-release licensed games if they have to renegotiate licensing even if they still have the game code (which is why Capcom and so forth generally prefer to develop games based on their own in-house character creations)… Most re-releases of licensed property just don’t make the money to make the effort worthwhile. Marvel Vs Capcom 2 was a noteable exception…