In a way, he's already been resurrected... well, not really, but the symbolism is close enough. He gets knocked into a coma ("dies") at the end of the second movie, and then is "resurrected" when he's rescued from the train station.

It's possible that he could be resurrected, I suppose; if he's been absorbed into the source or whatever, then he can be remade. But I hope they don't do that, because that would spoil it.

I wouldn't mind seeing another movie set in the same universe, but it would have to be set in a different time and with different people. The rise of the machines has already been covered in the Animatrix, but there are other things which a movie could be made about... like that bit in the Animatrix where they're converting some of the machines to their side. What was with that, anyway? It doesn't seem to fit anywhere near the storyline of the Matrix movies; presumably it's some time after them, or possibly before them.

In the Bible it said that Jesus took his physical body and made it spiritual, and only his believers could see him. So perhaps he left his physical form and went into a sort of digital form, where only the machines could see him.