Well there are a few things.
Presumably Meredith will survive the fire, we don't know for sure but she seemed resistant to flames.
Sylar though was left on the floor. Now it is possible Angela removed the glass beforehand which would allow him to escape.
(Arthur could survive after all if someone removes the bullet and return him to life)
Now based on what they said before Peter has his original power back. It is probably safe to assume that he does not have all the absorbed powers back like how Sylar lost his original ones as well since he still has the scar after dropping Nathan off. At the time Flint, Nathan, The Haitian, and Dr. Surresh were in the building. So he may well have acquired all their abilities. Coming within range of Sylar would give him most of his others assuming Sylar survived.
Remember the number one rule in comic books, if there's not a body, they aren't dead. They showed Elle's body and Arthur's, but not Sylar's......Even if there is a body they can come back.
Peter will become the terrorist of future Peter it seems. Every future or alternate peter had a face scar which means every one of them had at some point lost Claire's abilities, though in some cases they had regained them later. I bet he seeks out Claude first, perhaps we'll see the Invisible Man again. Of course coming near Claire will restore them.
Wonder what Ando's power would do to Peter's power.....yeah let him copy Ando's power so he can supercharge all his own abilities.....
Hiro has still lost his powers, in most futures HIro was gone. Peter might seek out Hiro and also see if he can find some way to restore Hiro's powers. After all future Peter had them.
Something else bothers me, Sylar mentions that he couldn't kill Claire even if he wanted to. So if that is true and Sylar took her power, and Arthur got her power from Peter, then we may see both again.
Elle I think was Claire's real sister. I do not think Bob was Elle's father.
Also Beverly was not her name, Micah's cousin's name was Monica Dawson.