Wholeheartedly agree with khoregard on all points.
I have REASON now and i'm really excited about being able to make stuff like this.
I don't know whether or not you are using reason to create this, but I've been doing a lot of practicing with it and I think its really fun when I can visualize and work out in my head how to make instruments that sound and phase like this.
Can't give you any advice myself compositionally, I'm still a fledgling when it comes to getting those ideas going on my own -- I turn to listening to other songs and picking ideas from here and there.
Regardless, the concept on this one is golden, keep up with it! It's already a strong mix with all but 2 or 3 instruments.
EDIT: I just got a really nice idea -- HAHA!
I realize that any time indexes have no doubt already changed in your song if you are currently working with it, but bear with me.
Right before 2:00, when you go from the second melody back to the first, you should do one of those sections where you dump the beat for about 15 seconds. During this, make the instument that is the progressive lead distorted, but not phased-so the notes are long and drawn out-and continue with a slightly modified version of the same melody, when that section runs its course and feels long enough, snap back into the beat, drop the distortion, bring back the phase and go to the next melody.
This has nothing to do with the remix at all, but I see it over here and I think it's pretty funny.