Interesting thread and interesting question.
3d would be nice but it often seems that 3d graphics, if not extremely polished or professionally done, have less life and character to them than decent 2d graphics. So I would probably stick with 2d just for that reason, unless an awesome 3d graphics team could be found.
The variety of zako and the variety of moves would be important, so that whether you're giving or receiving the beating, it could happen in a variety of ways and to/from a variety of characters.
When a character is defeated (whether it be your character or an enemy zako), instead of blinking and disappearing they would remain on screen, barely conscious or completely ko'd...but they could still be interacted with. For example, the zako might continue to taunt or kick the defeated player's character until he/she pressed continue or suffered a complete gameover. Meanwhile, a defeated zako could be picked up and smacked around some more, used as a human shield, thrown at other enemies, dragged or carried, etc. (no need to feel sorry for them since they are baddies after all).
They might continue to react until completely ko'd...and there might be ways to wake them back up, take them prisoner, and/or finish them off completely.