It'll be interesting to see if Neo keeps his powers in the 'real world' or if the 'real world' is really another part of the matrix somehow. Either way, I do think he was changed or something changed after his meeting with the architect. When they were getting off the ship and the sentinels came he said "something's changed I can feel them" and there was clearly something that happened to him as a result of their confrontation. The possibilities are entertaining.
btw how did morpheus get out of the building when Neo went in to see the architect? All those agents were still in the hallway and the key maker was dead. When Neo flew out the building he was no where to be found. But he ended up back on the ship.
