<font color = lightgreen>2) The Seraph is in the Matrix, but isn't really
of the Matrix. He is either a holdover program or some sort of "meta-program" like the Oracle, a program that edits the Matrix to keep it running smoothly.
4) Pretty damn fast to be blowing out windows with the sonic boom trailing behind him.
5) Yes, else they would have continued to attack Morpheus until they killed him.
6) Smith is
much more powerful now because he is controlled by no one but himself. That is part of Smith's new power--the ability to assimilate others and convert them into copies of himself. Check the other thread
here for more about Smith and how he relates to Neo.
Neo hasn't figured out how to teleport or transport himself between locations without using already-existing doors without keys. Maybe if he had several more years he could, but he has about 29 hours, or something like that.</font>