I like it. I much prefer this order to the opening scenes, it's more like how the first movie handled things (Xavier voiceover, credits, flashback, present). Exactly what I would have done (well, I still don't know if Angel's really needed in the big picture).
I do think a couple of your transitions could use just a little tweaking, like having the first shot of the street visible through the "eye" of the Cerebro door as we fly through. That seems doable with a matte and some filters. The cut from Angel's back to the Danger Room is also a bit awkward. I know you were avoiding that quick zoom-in on his wing-stumps, but maybe if you slowed down the end of the shot a bit, let us linger on what we're seeing, then surprise us with the cut to the Danger Room.
I hope you don't think I'm being overly critical, because I really do like what you're doing. X3's the first movie that I've been interested in seeing fans recut, just because there are so many things in the deleted scenes that could have easily made the film better. I very much look forward to seeing you and others continue this project.
As an aside, having only seen the movie once, I hadn't noticed how much better the verision of the opening theme in the movie itself is than the one on the soundtrack. And it's made all the better by coming after Xavier's voiceover now.