I get what you are saying, but it's a cheap plot device. Dreams within dreams within dreams (or realities within realities) gets old, and allows the writer to ignore rules that he has already established. The Matrix followed all its own rules. Everything was thrown out the window after that.
Besides, very few movies successfully use the dreams-within-dreams scenario. The Thirteenth Floor immediately comes to mind, but again - it follows established rules throughout the film. No cheats were used.
"I would like to see the agents at the end of the Matrix as a deep brown almost black silouhette with an orange outline like how the programs are represented in the sequels."
With all due respect, the first Matrix is perfect. I wouldn't touch it. Like the Prequels, the sequels should match the original film.
"The first Matrix will be untouched. I find it to be a nearly perfect movie."
LOL....I had already typed my response from the first page, and was pleased to see this on page two.
"The worst problem is that the second movie lacked any real subtext. The third at least attempted to incorporate religious allusions to the story like the original. The second is just a mindless thrill ride and little else."
Agreed. It was all setup.