Seriously, this looks amazing so far. The plotline is very cool, simple, solid, but with plenty of options.
And I'm sorry, but I think Munchlax as a starter would be just plain awesome. Actually, I have a recommendation for that event, though I'm not sure if you've decided to scrap that script or not. My understanding is that we'll encounter a Pokemon on the way to the lab and pick it up, so, what if you first entered a script where a question mark pops up. The player thinks he just heard a Pokemon, and wonders which one it was (list three choices). Whichever choice is selected, that is the Pokemon that crawls out of the bushes, wades out of the grass, or leaps insanely to gnaw on the trainer's face, whatever you were planning there.
Anyway, that way at least the player would have a choice (personally, I want Munchlax :))
Erm, and about starters, can I suggest Tyrogue and Misdreavous as the other two? Actually, I'd prefer Sneasel to Misdreavous, but this way you have that advantage triangle if Munchlax learns bite.
Although, I suppose you could replace Munchlax with Sneasel.
As for Darkrai as legendary, I'm not sure what everyone's so annoyed about. There's really nothing wrong with him, though I prefer Giratina, but he's even more cliche than Darkrai.
All in all, absolutely terrific-looking hack. I'll definitely be supporting this, and let me know if I can help.
Oh, and one last thing. Your maps so far are absolutely incredible, just because of those tiles. I am so incredibly and unabashedly jealous of your tiles that it's not even funny. If you guys make a rombase of those tiles, I will worship you.
Oh, and could you post a list of the DP Pokemon you're adding?
...okay that's about it. Don't quit, or I will hunt you down.