I would think that he gets most if not all the powers back. If you notice no matter how much they try to change the future, certain things remains constant. Future Peter gets powers back, we also see how he got the scar as well. Now we also may know why in the future he has a hatred enough of Nathan to kill him. Ando's also get's his red lightning that Hiro thinks kills him in the future. Peter probably just needs to meet up with Syler for 5mins and he's all set
Speaking of Syler, that's one thing that really bugged me this season. Between as I mentioned before his good/bad streaks, his love/hate story, and his parents. It really did make sense that Syler was their brother as Peter absorbs abilities, his father can steal them, and Syler can figure them out and take them. Then they were like "eh, no not really" and off on yet another tangent.