Hmm, I was looking at this before I joined. You're definitely a good spriter, and your work reminds me of some of the better stuff in the "It's Evolving" contest at Pixeljoint. I think a few could be done better, though. I'm not saying they're poor, but that you've probably gotten better over the course of making all those Pokemon. Most notably are 18, 22, 23, 24, 27, 28, 80, 81, 127 and 128. I could be missing a few, but I trust your best judgment. :P
It definitely looks interesting and I hope it comes out nice. I'll have to drop another comment after playing the demo, I suppose.
EDIT: Alright, I played right up until I beat the Team Magma Grunt. Obviously the story needs some changing, but I'm sure you were getting to that. One of my disappointments was that the region is still the same, just with different maps. While the Pokemon do give the game a new feel to it, that's severely restricted by the maps. In fact, this is why I didn't like Pokemon Quartz. The moves obviously need some updated. I don't think the first rival battle should be so hard. As there's not much strategy involved in a tough battle when it's just your starter. It just causes unnecessary grinding.
Hopefully a lot of things get remade. Overworlds, tiles, gyms, etc. With your abilities this hack has a lot of potential. I'll be keeping my eye on it. :3