Sylar's Power: First off, another technical point. Sylar lost a bunch of his purloined powers when Hiro stabbed him back in Season One. Fine. At the beginning of the chapter, he attacked Claire with his telekinesis and took her regenerative power, which restored him to full health. You'd think that would have restored those powers as well, since he learned how they work and all, but no. So the logical conclusion is that the sword blow permanently erased the powers he had stolen and left him only with his original ability -- except telekinesis wasn't it. It's true he was telekinetic at the beginning of the series, but it's this vague ability to "understand how things work" that's his power -- as "Six Months Earlier" showed us, he stole the telekinesis from that guy Brian in the watch shop. On top of that, though, there's the "hunger." We learn from the past that Sylar was able to control his "hunger" when he was feeling warm and fuzzy for Elle. Then he was able to control it when he thought Angela was his mother. Then he was able to turn it into something else entirely through empathy. (Remember Arthur had Sylar's power too, or should have, from Peter, and we never saw him afflicted by the "hunger.") Then he became a killer again anyway. On top of that, Peter took his power because he thought "understanding how things work" would help him save the world. But that power is complete and utter bullshit -- Sylar didn't know fuck-all about how things work, or he might not have been used as a pawn by Arthur, Angela, and even Elle.
The Formula: Why didn't Primatech destroy it? I asked this in the very first episode, and it was never answered. If it could only be used for evil, why didn't they simply get rid of it? Anyone? Bueller?
Mohinder: Look, you saw it for yourself.
Incredibly Heavy-Handed Religious Overtones: Look, I've watched plenty of ridiculous TV in my day, but when you're completely ridiculous and yet you take yourself so seriously that you insert the most somber religious passages and imagery into your show and unironically think it fits? You've got problems.
That's not even half of what I could have written, but I'm not getting paid by the word and I want to move on to the episode. But seriously, with a budget as big and a mythology as extensive as this show's, what's the excuse for not having a dedicated continuity editor? Or for not firing the one you have and getting someone who can handle the job?