What's with the Loop. Maybe the Loop train in Part 1 was sent By the Merovingian, THINK about it, it ALSO said LOOP, AND the train ACTUALLY Hit a LIVING Person, and kept going, meaning no inncocent slave mind was controlling it.
Maybe the MErovingian Brought AGENT SMITH back from the Dead.
DOes'nt The Mero hack programs??
maybe Neo goes to see the Oracle, but he is betrayed, by someone, and drugged or something, or maybe, since tha Oracle says Neo is caught between "your world and Mine", Neo is trapped in the Matrix, while his body is in a coma, and he can't use his powers, cause he's not really plugged in, and this is how Mero gets him. I dunno, just rambling thoughts....
maybe Smith is laughing because he takes over the Oracle, or he gets his fortune told. Or maybe he's laughing cause the Oracle's shell has changed, or he meets the Mero, or any one of a million other possibilities. i dunno, maybe he just heard a joke that he finds funny.
"So, a priest, a rabbi, and an oracle walk into a bar..."