Part 2 would have been fine if they did a different part 3. I was convinced and excited at the prospect of a layered reality. We had the kid give the bendy spoons to Neo, Agent smith downloading himself into someone living outside of the matrix in Zion (HTF is computer code supposed to run in a human brain anyway?). Then at the end when lightning bolts shot out of Neo's hands and destroyed the sentinels there was no way at this point he was not still in some type of matrix.
Sadly when part 3 came out all it did was double down on a stupid plot. Both movies on their own are good if the other had a different plot, but instead they both ruin each other and do not exist IMO.