I think Yoda in ESB was there to show Luke (and by extension the audience) that the force is something beyond the physical, and that you don't need to be physically big and strong to make a big difference. The audience isn't expecting this shrivelled up frail alien to have any real power at all, and then he raises the X-Wing out of the swamp, not with brawn, but with the power of his MIND.

Yoda represents the intellectual and the spiritual. To have him fighting at all undermines that IMO. He should be like a Jedi monk, rather than a Jedi Knight.

It's worth noting again though, that I don't think Yoda should even be in the prequels. He should be known to the audience as "That mysterious Jedi Master that the most gifted Knights go off to be trained by occasionally" but we shouldn't actually meet him until ESB.