I watched season 2 over the weekend to get ready for the new season. I had complaints last year about how it started off but it turned itself around and I liked the way it finished. However, if you watch the alternate ending, the ending I'm sure we would have gotten had it not been for the impending writer strike, the season was headed in an entirely different direction than what we got.
Neither ending, though, pointed to what we got last night. I wasn't shocked that Peter was the shooter, it was, in fact, one of the few things I liked about the episode. I didn't like pretty much everything else.
I disagree with you, Bill, I think Mohinder's plot is terrible and possibly one of the two worst things about last night's episode. The second was Sylar's attack on Claire which completely didn't fit within the flow of time in the Heroes universe and wasn't explained in any way...it just was. And now we either have to just own it or we have to wait for some flashback episode that decides to fill in the missing 10 minutes between season 2 and 3. Terrible.
The plot with Niki was a runner up for worst. This is one of the issues from last year where they introduced new heroes without tying them into any other plot, basically, it's one of the things Kring owned up to in the article linked earlier in this thread. Last night they did it with this new character yet they haven't resolved the whole Niki/Monica/Micah plot. Does Niki suddenly have a twin? Is she a clone? Do I care? Weren't Niki and Jessica enough, they couldn't resolve Niki's plot so they needed to invent a character just to keep Ali Larter on the payroll? Are they going to abandon season 2, like it never happened? Bah.
Oh, one more high point, for me at least; Francis Capra was on the show last night. I'm hoping he's back for a few episodes and I hope they put him in some scenes with Elle. Loved his character on "Veronica Mars" and Capra's character was at his best when he was on screen with Kristen Bell's Veronica.