I sometimes wonder about the way the emulation handles the tracking of the optical devices. (wich may be why the windows mouse acceleration messes things up worse)
Some games for instance, used gears to increase the speed of the pulses. This may be one reason that those games require such a high level of spin in the emu's- while other emulated games are more sensative to movments.
Also, the way that the real arcades may have read the devices may have been different. Some may have took the puleses, and moved the characters one increment per pulse... while others may have acted more like a mouse, and calculated the pules into time/distance to get the acceleration. While simular in nature, the added accumualite of constant acceleraion will add exponentially to the values. Im probably describing this incorrectly...
Do I make any sense? : )