^^ I understood it as he can see through the code (which we saw endlessly in the sequels) but not really manipulate the very matter of the Matrix. However he DID alter "reality" when he resurrected Trinity. You could also argue he did this when he deactivated Sentinels in the real world. The problem with the rave scene is just it just goes on and on at a point where there hadn't been any action for quite some time, plus I didn't feel the graphic sex scene needed to be in there. If they had just had the dancing starting then cut away to Neo having the vision it would have been enough. I get that it was supposed to be a 'celebration of life' and all but I just wish it wasn't in there.