Actually, given the myriad of characters and broad fictional elements used (time travel, precognition, etc.), I think they've been pretty good about the plot holes so far. Nothing really major has creped up and the minor ones end up being rather frivolous.
Anyway, good point about Mohinder not taking out Sylar. Would have been the perfect opportunity, but of course, we'd lose a really good villain. It's boils down to 'for the sake of the story, we let Mohinder be dumb for a few seconds'.
Ah well...I wasn't too bothered by it...lol, but man, Peter would be pissed if he found out what happened...
"Dude, why in the world didn't you kill him then?!"
"Ummm...oops?"