Remember, none of these events happened to scarface Peter. in his timeline Clair wasn't at home when sylar attacked (although what prompted her to leave is another question as Nathan wasn't shot in that timeline) so Sylar never attacked the company and the level five inmates never got out, which meant that Arthur had no one to 'translate' his thoughts into orders, meaning he was left as a vegetable.
Wait that means for scarface the big bad who created the formula wasn't Arthur. Which means that either Mohinder perfected it on his lonesome or the person who releases it to the public was someone else - not Arthur and none of the level five inmates, so that leaves Adam or Angela and as Adam was fairly disapproving of the formula and is dead in the current timeline that wouldn't make for a very interesting story twist - so maybe it was Angela all along and Pinehurst will turn out to be the good guys.
Actually, I don't think Maury is dead. I think it was a staged illusion fake-out to convince Daphne to go along with it. Otherwise, African Isaac's painting of "the four big bad guys you need to stop" was kind of pointless since one of them was most definitely Maury.
While it's a very clever, and indeed very likely idea, I really hope its not the case. This series has already had enough *omg he's dead audience all get upset now... oh wait no he's not we were only kidding LOL* moments.
1. Nathan (who's miraculous recovery still hasn't been explained)
2. Clair when sylar came to call
3. The entire series is kind of based around it with Arthur
4. Matt and Daphne
5. Peter being thrown out a window with no healing facing certain doom then *addbreak*