I am a big fan of the Matrix. I really enjoyed the first two movies and am looking forward to the third.
Consider this, what if either Neo has some form of ESP or his bonding with Smith might have affected both of them.
If you remember in the first movie that Neo destroyed Smith by entering his program and some how causing a deresolution. That union might be the cause of what happened in the second movie. There might have been a accidental mixing of abilities that exceeded what either could have done alone.
Smith having the ability to travel through the the phone connection which is the direct connection to humans brains and somehow interfacing with a human and taking control inside his brain is really very possible if not plausible. Remember that the human brain is a biochemical computer of sorts. Sense his program has become a virus of sorts then it is very possible for him to travel into a brain and take contol.
This union could also help explain how Neo got his powers outside the matrix. It is also possible he has telekentic powers. We also must remember that in the many of hundreds of years that humans have been enslaved by the machines and the tampering that the machines have done to specific humans might be the cause of neo's evolution.
The issue of why Neo fought in the playground with Smith is he had destroyed him before and was not expecting him to be able to handle him. He wanted to destroy him again and make sure that he would not come back. It was not until he was overwhelmed that he decided to flea. He is trying to change the matrix for the better. His power over the agents might also have made him rather cocky and willing to fight instead of running.
In my opinion there is no Matrix within a Matrix. The people of zion are fighting for their freedom and Neo is there savior. But this is all speculation of course and I hope the final film will reveal the truth.
Sam