Like others in this thread, I really didn't like this episode. In all honesty, I enjoyed Chuck and Reaper this week more than Heroes.
Heroes just seems too disjointed and scatterbrain. The writers seem like they can't decide how characters should act in certain situations. Motivations and personalities change from week to week. Power usage and (or lack thereof) change from week to week. Heck, I wish there was more power usage.
Peter should be kicking major butt with all the abilities at his disposal - invisibility, mind-reading, flying for pete's sake (no pun intended). Obviously his wide range of powers can signficantly change the outcome of scenes but if the writers aren't comfortable with that, they shouldn't have given him all those powers in the first place. The worst thing in a superhero story is selective use of powers, at least not without some kind of explanation.
Power inconsistency aside, I'm just becoming annoyed with some of the other characters. As much as I don't like the snooze twins, why Maya became his disciple so fast really bothered me. And as someone else mentioned, those scenes were creepy in the not-good-kind-of-creepy way. I feel bad for Zachary Quinto/Sylar. He was doing everything he could to hold those scenes together but he must have been like "what the heck is this" when he read the script. I would have preferred that he just kill them both and be done with that story arc.
I really don't like the Company/Claire/Bob/Claire storyline either. Claire has been totally misused this season. Mohinder seems to not remember anything from each previous episode. I also don't feel Bob adds anything. The Company storyline has been a complete bust IMO. Sure there's a super powerful virus about to be released but the Company just doesn't come across as that sinister on-screen. The "faces" of the company (Bob, Ellie, etc) are more annoying than anything else. I just don't them seriously to think that they are responsible for these far-reaching world dominating plans.
The Monica storyline went from pretty cool with some potential to a throwaway.
But by far, my biggest complaint this season has been relative lack and inconsistent use of power usage. It's just so frustrating, especially with Peter and Sylar. They are the strongest characters on the show are they have been dealt lame storylines.
They are right - season 3 better get back on track.