See I don't think that's actually how the showdown ends between Sylar and Peter. After Isaac stressed that he knows how to stop him, I believe that the showdown comes either at the end of this season or at the beginning of next.
Personally, I think that we've been shown how impaling the brain can stop a Heroes powers (read: stick in Claire's head, glass shard in Peter's), because its going to be important for killing Sylar. After all, he doesn't have the regenerative powers that those two do.
I'm still really curious to see how Linderman plans to use Micah to help "save the world." No ideas about that one lol...