FbaXXX is best for emulate Capcom and NeoGeo games as it run them at very good (best/original) speed - its much more optimized for this 2 types (frame skip 0 all the times).
Mame from other hand support wide range of games (manufacturers) - but for price of performance (in some of them).
Try run this games in Mame (with frame skip on) to see how this was solved/done (shadows for example)
As for FbaXXX try to set Flicker filter to 5,turn on soften, maybe play a little with CPU emulation speed -but again - everything is as should be