Seems like you've missed some episodes. Peter has known Adam for more than five minutes. He's been his sole confidant for months now, and--more importantly--has been the only person in the know to earn Peter's trust. He may love Nathan more, but he doesn't side with Adam out of love, but rather because he seems to have good intel. The Company has indeed been sitting on top of a super-virus.
Adam taught Peter how to recover his memories using his regenerative powers.
If Grandma Patrelli can shield her mind from telepathy, it's likely that all of the old-school heroes can.
Having said that, most of the characters in Heroes are indeed inexcusably incapable of connecting the dots. Mohinder has failed to develop into a worthwhile character. He should've been bumped off a long time ago, but tonight would have been good too. On top of not being an actual hero, he's also been consistently stupide and no longer has any excuse for being so naive. He's basically a damsel in distress.