It gets stranger when you read the books from the past Worlds. There are a lot of hints that the Princess is a bomb throughout the game. There is one book that says that when Tim finds the princess the world will change, which would be the same with a bomb obviously.
It also then makes sense what the "mistake" is that Tim made. He could be trying to stop himself creating the bomb. This would sort of explain the whole time manipulation element.
The interpretation that Tim is one of the scientists working on the bomb, also backs up the point I mentioned earlier about nobody thinking they are the bad guy.
Of course, I've probably missed out a heck of a lot of things in it. I'm going to play through it again, I think, just because the game itself is amazing. It is a truly amazing game overall. It looks amazing, plays amazing and is extremely thought provoking. Especially for an Xbox Live Arcade game.
I <3 Braid!