Yeah, that was a pretty cool episode. I liked how they used Hiro's going back in time to parallel the other events that were happening at the same time to introduce the other heroes back stories.
I think the reason Skylar removes the brain is to somehow see into their souls and figure out how they work. In that way, he can steal other's powers when he can study their brains. It's a long shot, but that is my theory.
As for Bennet, he seems to have a pretty extensive operation going on. Maybe he's a government agent that has been aware of and studies 'gifted' people. Maybe he was apart of the project that may be responsible for the marks left on a couple of (if not all) of the heroes.
And yeah, I think that in some ways time is inevitable for some people. It seemed that he wasn't able to beat time with his current knowledge of bending time. Maybe by the time NY goes BOOM, he will...
Next weeks episode promises to be a good one with another good ending; too bad it is the last of the year.