As for thoughts on the episode itself I liked it or at least I think I do - with such a long wait I was happy just to see any new episode. I plan on rewatching it but part of me thinks that maybe too much happened last night. I thought the Hiro storyline was done very well (by far his storylines have been the strongest I think) but the Petrelli storyline was just all over the map.
I was confused between future/present Peter, Peter apparently stored in some other guy's body, Linderman being back (although I'm happy he is), Jessica/Nikki/Tracy (did Linderman heal her too?), all the guys on level 5 and who they are and why there are there (and why was Bennett kept there if that was supposed to be the worst of the worst people with super powers).
I like some of the twists that seem to be coming out of that storyline like learning Ma Petrelli's power (at least one of them) and her bombshell at the end but I would have liked some more build up to some of those events.