I think a good idea (and something I thought they were hinting at in Reloaded when Neo is able to stop the squiddy) would have been the idea of the Matrix within a Matrix, ie those who “reject” the main programme awaken into what they think is the real world, but they are still inside the Matrix (ie Morpheus et al on his ship, etc). I had hoped that Neo would turn out to not be human at all, but a self-aware computer programme that ultimately has to sacrifice himself in order to destroy the Matrix (taking it down with him) and free humanity.

As it stands, I think the Matrix sequels are pretty rubbish, give or take the freeway chase in Reloaded which is very well put together.