I liked the new Colonel. He came out very jerk-ish in the beginning because he was walking into a combat situation and wanted to establish a clear chain of command. He had no time for niceties. He warmed up as everyone went about their jobs, with superb performances, and became rather likable. But I have to agree with what is above, I'd hate to see him next season, for he takes something away from Shepherd.
The Genii (It seems everyone spells them differently) subplot was...a bit forced, but I felt it belonged. They were the other major villains in this show...I just hated the "The Wraith have hit us so we have nothing more to worry about" attitude. It made little sense and it hurts the Genii's role as saviors to Pegasus as they have wished. I'm hoping it was just a front to throw Weir offtrack.
As to the ZPM, I'm not surprised at all. O'Neill is not a selfish man, and he knew the crew of Atlantis were about to be wiped out. I'm more surprised he got away with sending it, as the decision is not ultimately his.
The attacks on the city were nice, and some great detail on the city. Some of it was a little grainy but very nicely done. The last few minutes, though, did harm it for me, as we can all guess how it's going to be resolved. But if the two part season finale, and the season 2 premiere were watched back to back to back (to back?), it might fit better. And to keep with my other posts this day, I gave this episode a B+.