One of the things that always annoyed me about 'Five Years Gone' is that we don't see the fight between Future Peter and Future Sylar at the end of the episode. More importantly, we don't know who wins. I just finished re-watching the episode and just when Present Hiro teleports with Ando back to the present, you can hear a scream.
Now, this may be Mohinder's scream as you can see him trying to hold back the door but it really sounded like Future Sylar. It actually sounded like the kind of scream heard when people get Sylar'd. Maybe Future Peter gave Future Sylar a dose of his own medicine. I think that this was maybe a little hint that Future Peter, in fact, won and will win when they have their massive awaited battle.