After reading some of that thread here is my response:
A good document to read is
Arcade Emulation How-To.
Basically, the issue that people have with speed stems from the fundemental way you are playing it - on your computer. You aren't just loading up the game into memory like it's half-life or quake. Mame is emulating the hardware of the machine and then it's running the software (or roms) on that emulated hardware...and that's not counting 3d acceleration (which is absent in MAME I believe). That's a lot of processor power required for a newer machine like Area51 and Cruisin' USA.
The whole concept of emulation is to emulate just the hardware of each machine - you shouldn't have to know the actual code of the game in question. Perfect emulation should be able to just load the roms into the hardware and the game would work 100%.