  Well. I guess I can like the movie. It wasn't really all that bad. I wish I had a better quality bootleg of the damn thing but I can't complain. In the Matrix code is Green. In the real world, code is Orange. I can't think of anything else. Maybe since he went to go see the source he learned to see "real world code" compared to "matrix code.
" Even Smith was orange in his eyes after he downloaded himself into Bain. (the actor who played Bain did a great job in imitating Hugo Weaving) I don't understand that either. How can he download himself onto a brain? Like Slashdot.com mentioned, there has to be some sort of compatibility issue right? I don't know. "It's not a vary big leap from powers in the Matrix to Neo's powers in the real world. All the human bio-electricity flows from the pod fields to the Source, and then it is redistributed back to the Matrix along well-defined channels. The humans plugged into the Matrix then have experiences, from which they have emotions, and their emotional energy flows back to the Source. What I haven't mentioned is the machines. They are parasites on this energy loop between the humans and the Source. We should also notice that Neo's apparently "supernatural" abilities in the real world are strictly limited to affecting machines.
He doesn't fly or do kung fu in the real world. The reason for this limitation is that he is merely tapping into the energy loop and...modifying it. Just like in the Matrix, where he modifies the energy loop to defy gravity, etc. " In Reloaded he is driven by Love (i.e. Trinity). In Revolutions he is made into the savior, Jesus. He sacrificed his life to save all.
Too bad she died but I think it was necessary so that he wouldn't be distracted from doing what he had to do. There was also the balancing of the equation. So there are two variables that are dependent on each other? (Neo vs. Smith) As one gets stronger, so does the other? Mobil Station. It was the "connection" between the Machine City and the Matrix. Kinda like Limbo (River Styx)? Merovingians and Club Hel. Sereph, the wingless one. Deal with the Devil. Oracle's Eyes while eating two eyeball looking olives. 
