This looks like an interesting project, I might just try this out when the beta is ready. Oak's Research area is a nice addition. I'm sure you'll be proofing your maps and stuff since you said these were rough map designs but the tile right above Oak's door is wrong, lol unless Oak is just that cool and wanted some half windows.
Edit: Eh I wasnt going to ask but, you said you're rebalancing all the pokemon to make them useful, what ideas do you have for Magikarp, I know he evolves into Gyarados. But Magikarp himself learns splash, tackle, and flail and I don't believe many people use him widely because of his move set