Sound seems to be more accurate in MAME though, and some games in GnGeo and FBA2X have bugs where the sound stops working (eg. Aero Fighters 2+3).
Unfortunately to play all Neo Geo games well, you seem to need to use a combination of MAME4ALL (more accurate sound, configurable controls), GnGeo (faster, cache games sometimes smoother (Metal Slug 3)) and FBA2X (runs the bigger/more recent games that MAME4ALL doesn't, faster).