This reminds me of when I collected Beanie Babies as a kid, and drew up a list of all the animals I could think of that hadn't been made into one yet. I suppose that says something about Pokemon in more ways than one...
Anyway, cool thread. Let's see...
--That one virus that looks kind of like a spider-robot. I saw there was a microbe Pokemon in B/W (shades of Bowser's Inside Story for me), so why not?
--An actual starfish Pokemon. Am I the only one who thinks that, even by the current generation's standards, Staryu/Mie is really weird? It doesn't have a face, and it's... made out of precious gems, or something.
--On that note, a sand dollar Pokemon. It could be a Magikarp-type thing and evolve into... er, a mussel? A Eggecute-esque barnacle Pokemon? Hey, I live in the Pacific Northwest--cut me some slack.
I have other ideas, but some of them are ones I'm actually planning on implementing into a very heavily Pokemon-influenced book at some point, so I'd just as soon they weren't Pokefied. To be honest, I'd prefer it if there were more Pokemon that were at least superficially "original", or at least based on Japanese stuff that I'd have to look up and educate myself with. No more of this "change its color and one letter of its name" crap.