That's great, I promise I'll do my best to help you work out the details, although you seem to have everything under control. ; ) I was amazed with the length and quality of your post. Such an update is inspiring. There were only a few minor things that I wasn't sure about. First off, I think you might want to cut down a little on Officer Jenny's hair. The hairstyle you chose seems to make it look longer than it actually is. Secondly, I love the overall design for Team Rocket's balloon, but as you stated it's pixilated. I'm sure you'll do a great job with it when it's finished. Also, Meowth looks a litttle small in porportion to Jessie and James. Perhaps you could use a ripped OW from HG/SS? I'm sorry, don't know that much about that sort of thing.
On your videos(which have me very excited by the way, I love videos from Pokemon games), Azumarill isn't really a Kanto Pokemon, so are you sure you should include it in the title screen? And I actually love your Who's that Pokemon, didn't expect for you to do that, very original indeed. Although, once again, Unown isn't really Kanto. Lastly, I actually don't like the Pikachu, not just because it's a little glitchy, but because not everyone will want a Pikachu on their team. But if you want to keep it, I doubt it will pose as a big problem.
I must admit, I'd never heard of anyone got to such lengths for a Pokemon series game before. I'm proud to support this game, and I hope that you'll tell me(via PM to prevent stealing) when you need any help from me, anything at all.