Seriously. There wasn't really a fight there. Also, Sylar getted stabbed was kind of anticlimatic. I think it would have been all kinds of awesome if Sylar was about to off Peter and a sword blade suddenly appeared in his chest. He's completely mystified, turns around, and time-phased Hiro is staring him down.
As for timeline stuff: I think what they went for a sort of Legacy of Kain style timeline. That is, there aren't multiple timelines, per se, but one timeline that's always trying to adapt to the changes being made.
"Drop a stone into a rushing river - the current simple courses around it and flows on as if the obstruction were never there."
In other words, the predefined timeline is pretty difficult to significantly alter. If you make a change, it will simply work around it and try to get back on course. Originally, Sylar would have been the bomb. Future Hiro went back to save Claire, thus giving himself the opportunity to kill Sylar and prevent the bomb. But history simply adjusted a few details, making it so that the bomb would still go off, even with the alterations.
The pebble he dropped into the timestream wasn't enough to divert it. Instead, they needed to drop a boulder - a change in everyone's destiny, not just Claire's. Both Peter and Sylar had the potential to be the bomb. If Sylar had managed to steal Claire's powers, then even if Nathan had showed up to help his brother, Sylar would have blown up. It was set on that course and was pretty determined to see it happen. The future wasn't changed by one event, but by a series of events.
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