Regarding what you could put as a reward for basically "beating the game" aside from Orre Colosseum, maybe Robo groudon, Robo Kyogre, and a Mew that knows Shadow moves? Y'know, like that one battle in the 95+ area. I did NOT expect to see something like that up there! But it makes perfect sense.
Also, on a scale of 1 to 10, with 1 being copy-paste easy, and 10 being completely impossible, what are the chances of a mod (not necessarily yours, but mods to this game in general) importing the excluded areas back into the game, like the caves of Pyrite, The Under, and The Deep as postgame/optional content? Seeing as you broke Versus mode, I was wondering if there was more 'free data' to use now, or if that's simply too hard to do with the current tools available. I'm not sure about the mechanics of editing a file like this, only that it seems like you can't "add" more space to the 'disk,' either because that messes with memory calls, or because the original XD already filled the disk to the brim.
Edit: Oh, also, just a minor question: Did you ever consider making the 100th battle theme instead be the song that plays in a Vs. Battle? Since it's kinda appropriate, considering the model used, etc. and it's not used anywhere else. Or was that scrubbed along with the rest of the Vs. Mode data?