The Charles stuff strayed into 'matrix 2 architect' territory for a moment there which was a worry. Maybe they were just planting more seeds for season 2 ala "there's someone worse than Sylar."
If i recall correctly Peter told Nathan that he couldn't control the power, then he said he couldn't do anything. I guess the only options to save the city were move him or shoot him. Although it might be possible that shooting him would not have the effect they were hoping for. What I'm wondering is what happened after liftoff....Did Nathan let him go and retreat to a safe distance? We know he can move around up there pretty quickly.
Re: Candace - it was probably just to have the audience quickly understand what's happening and move on. If she morphed to an apearance we hadn't seen before people would be confused and start up with new crackpot theories.
the reveal of Mr. Bennett's first name - I certainly missed that...What was it?
Claire convinced Nathan to act, Without Claire Nathan probably would have let peter die. And also Claire being alive prevents sylar using her ability so that hiro could stab him. Granted Sylar has retreated to fight another day - But hey he didn't explode so thats a plus.
At the point when Nathan learned of Linderman's death he was probably more relieved than anything else - he wanted the man dead. He had a best of both worlds scenario, His puppeteer in things political was gone and he still attained his position of power.
So the major talking points afterwards were of course no one checking on Sylar - or even noticing the blood trail. And Nikki actually doing something cool.