The more I think about the movie, the more I like it.
I still dislike the Zion plot (or at least the movie’s decisions on how to portray them), but I looking around at some suggestions of what the movie could have been (such as Mr. Butter Lover on aintitcool), I’m glad it didn’t decide to do that — i.e. Neo becomes a true superhero, showing huge power increases over the matrix, etc..
The first time Neo used the full force of his powers (jumping into Smith), he caused the smith fragmentation problem.
Everytime he flys, he warps space around him – in the end of the movie, we see the horrible damage that this power causes to the matrix.
I like that tie in, the use of power destroying, That even though Neo knows the rules of the matrix, he cannot yet “re-write” the Base, or base physics (since those are controlled in the source, I would think). He can bend the rules (or break them to the detriment of his environment), but he still has certain boundaries. A much better solution than Neo having sword hands or blink and have people turn into dogs or anything else.
They could have gone a bit further, perhaps — Shown Neo testing his power boundaries, etc – but seeing what they did with the Zion storyline, I’m happy with vague and loose plots from the Bros.