Also, I didn't like that Isaac's NYC-exploding painting didn't come true. I loved the idea that whatever was painted of the future ALWAYS came to pass, just not always in the way we assumed it would be.
But this is the FIRST time the painting has not come true, and that disappoints me. I think it would've been MUCH more interesting had the producers actually allowed NYC to blow up in the end.
One of the biggest themes of the entire show (yes, there's themes: they don't just do things because it's bad ass) is that history isn't set in stone and that we can defy fate. The way they made their point is by showing fate (Isaac's paintings) winning the battle against free will repeatedly throughout the series, but having the will of men (Peter's, Hiro's, Nathan's) defeat determinism.