@mforester another cool thing they could've done, is have Neo realise that while he may be a god inside the Matrix, in the real world he's just another guy, and decide that he wants to stay inside the simulation where he'll be more help
Then have them protecting his body while he's jacked in, or something. Would've made more sense than him somehow being able to use his powers in the real world, like at the end of the second film (did they actually explain that and I wasn't paying attention?)