Sonny from I, Robot finds himself in the Matrix one day. And Morpheus quickly realizes that this strang new appearance might be a sign of takeover just like what happend in his world. (See the AniMatrix) Morpheus and Trinity immediately insert themselves into the Matrix to kill it.
Sonny retains all of his abilities shown in the movie. Morpheus and Trinity are unarmed but have there powers and abilities.
Yes, in the bathroom fight with Agent Smith. They're also better fighters than Sonny. Well, atleast Morpheus is for sure. But Trinity did okay against an upgraded Agent in Reloaded with minimal space.
I'd say the only clear-cut advantage Sonny has is strength. And that's lifting things, not striking.