When I first built my 1.4Ghz Athlon machine, I found these results:
DOS + DOS MAME = Very poor
Windows + Windows MAME = Very good for 95% of games
Windows + DOS MAME = Perfect!
I found that DOS MAME running under Windows gave me the best performance. eg, Stun Runner was really bad with Windows MAME, but I got a 100% framerate with DOS MAME under Windows.
This was quite a while ago (remember when MAME v0.37? had all those betas?). I cannot explain why DOS MAME out-performed Windows MAME. Nor can I explain why DOS MAME in pure DOS was crap (from memory even PacMan didn't run at 60fps).
I still use Windows MAME, as using DOS MAME in Windows used to cause a horrible repeating noise when I pressed escape. Plus I preferred the video modes selected by WinMAME.
Anyway, so in my experience, using pure DOS was just not an option.