I don't think I would have time to participate in a role play now that my life is getting busy again, plus timezones (I don't want to keep people hanging), but I'd like to offer my opinion on what would I think would be an interesting RP.
First off, I'd say the region doesn't matter too much to me. I voted Kalos, just because I played X and Y most recently and it makes more sense when having 6th gen Pokemon. Second, yeah, no legendary Pokemon. Imagine if someone was a Celebi and decided to time travel through your Roleplay.
I thought the idea that the group creates a list of Pokemon for the person to choose from was a good idea, just because it seems fun, but the player should have the right to refuse the list if they truly hate it.
Multiple species shouldn't be a problem, and the trainer control should be the same as in the anime imo.
My idea for a plot, if you want ideas, would be that the human race is greatly diminished, leaving Pokemon-kind to roam freely through the ruins of what was once human society. Many Pokemon have never encountered a human before have heard extravagant stories of them being monstrous, scary beings, or maybe heroic and just saviours. The RP begins in multiple places. Some PCs being wild Pokemon, maybe a few being the Pokemon of PC trainers, and of course a few PC trainers. At that point my lame creativity runs out, but I'd imagine they might together all investigate how the downfall of the human race came about.