Wow, glad this thing is still up. I thought it would be gone for sure. I'll post my shit and then go back and comment.
First off, thought it would be neat to do one where the starters were a psychic --> fighting --> dark cycle rather than a grass --> fire --> water. Sure I wasn't the only one with that idea, but what the hell. Machamp couldn't be a trade evo in this version, though.
For the rest, at first I was just doing my favorites, though I thought it would be too much normal/psychic/ghost, but then as I went along I noticed a theme building and went with it. The region shaped up to be humid flatland. Lots of mud and rain, but few rivers. Sort of like a marshland that had been drained out.
Since I tend to favor ghost types, it seemed reasonable that this might be a place where humanity had once lived but had been abandoned-- maybe by a natural disaster. I was picturing Hyrule field after Link first becomes an adult in OoT, if that means anything to you. Poes everywhere, creepy ambience. Hence the legendaries are Yveltal, since it was just announced as 'the destruction pokemon' and Darkrai, since it's essentially the legendary of nightmares-- it's not a ghost, but it makes more sense than Giratina. Anti-matter doesn't really fit the theme.
I also omitted ice-- though I suppose there could be an ice gym leader. That would be an interesting challenge. Since dragon would be so powerful without fairy or ice to slow it down, I suppose a the E4 champion would take a page from Lance's book and go heavy on the dragon.
Other stuff: I tried to avoid man-made looking pokemon except for those based on ancient devices. Bronzong and Siglyph seemed to fit, but unfortunately Chandelure (one of my favorites) or Magnemite didn't. I also fucked around with certain pokemon's evolutionary tendencies. Made of few of them one- or two-stage pokemon when really they were three. It just seemed to fit.
Anyway, I worked on this thing for hours, so please let me know what you think.