Theory
Look, no one can deny that Keanu's acting was especially wooden in Reloaded, even more so than in M1 {sorry Korri!}. Most have put this down to poor acting skills, or possibly frustration at the long shooting schedules. But isn't it possible that this was deliberate?
Consider - there is some sort of "connection" between Neo and Smith. Consider also that Smith has been acting strangely {that is to say more human} of late, such as his manical laugh in Revolutions.
So isn't it possible that when Neo jumped into Smith at the end of M1, Smith took some of Neo's humanity, and Neo some of Smith's AI?
Just a thought