In some cases nothing...even some Taito's use the Midway boardset with an adapter attached. Sometimes people want the Taito since I'm not sure Midway made a cabaret, and in some cases people prefer the Midway since it has a nicer Cocktail table layout. Totally you're preference but for the most part the game is mostly the same.
Only major difference is Space Invaders II (not part 2 - thats Deluxe) - thats only in Cocktail form and the major difference there is that the two players can play against each other.
1) Many people prefer Midway cocktails given the orientation of the joysticks (virtually up/down) vs. the towards your stomach angle of other cocktails.
2) Midway have 19" vs. 13" monitors
3) Scoring on the deluxe version is slightly different between Midway and Taito IIRC (dont own one so don't know for sure)
4) Dual combat mode as stated above for II)
5) Taito uses short joystick, Midway uses a rotating lever.