I dunno...I'm with Steel Wind. I kind of liked this episode, all except the very end. I'll get to that in a bit.
As for the inconsistencies...I had some nagging doubts all along about how the linderman/Angela/Nathan relationship worked, all the way back from season 1. Linderman was trying to have Nathan killed, only to turn around and get him involved in the Scheme? Why? He seemed like the mastermind behind it all...until Angela started to seem like the mastermind. I think ret-conning Arthur into the backstory helps it seem more plausible, and gives it some more depth.
RE: sylar's retrofitted conscience...he's always had it. The episode with his mother tried to show him as having a soul, small and twisted though it was, and to explain him away as a product of his upbringing. And I thought that episode was pretty good. His current plotline is a continuation of that idea...I just hope they realize that it's gone far enough, and he should never be a "hero"...he's still a serial killer, and an egocentric bastard. You don't just "get over" that. As for his "new" old power...all we saw the guy do was shatter some glasses. Maybe that's all the power is good for. We HAVE seen Sylar inexplicably shatter glass; back in Season One when he smashed through his cell window to grab..um...the girl with the Super Voice. Eve?
As for the ending...I hated it, because it's another bait-and-switch. Release Adam Munroe! He dies in the next episode. Give Peter Sylar's hunger! He loses all his powers the next episode. Hiro learns the Company's dark secrets! He loses his power and is stuck in Africa, so can't tell anyone. That, or he teleports away (in the nick of time!) in the first 30 seconds of the episode. I wish the writers would just get out of each others' way.