Matt... I like you man, but ****
The story is building up so smoothly and it's supposed to be this way. The writers are supposed to tell you a story and they are doing their job in a great manner, if you ask me. Chronology is not a rule, but a tool for the writer, the same goes with Deus Ex Machina. If you know what you are doing and if you know how to use that tool at your advantage you can have a clever way of storytelling that is quite out of the norm. Heroes is never on the norm. It's a series about Superheroes.
You should jump in and watch The Melancholy of Haruhi Suzumiya... it's an anime but then again it's not just cartoons for kids and that anime has built a great cult in the genre... All of the episodes are messed up but the story still flows naturally... same with the movie Memento... if you know what you are doing you could have great pieces like Stardust (uses a lot of Deus Ex Machina) or you could have ****ty ones like Harry Potter and the Deadly Hollows (the same as Stardust, but done in a crappy way)