Hey, peeps! I was surprised with the amount of work that has been done so far, so I thought I'd make an account so I could say a few things.
Firstly, I know this might have been mentioned in those 34 pages of comments so far, but if you're looking to fill up a few holes in your dex you could always
ask permission from a few folks over at dA. Us sprite artists are usually flattered to hear their things are being used, especially if it's for something as high-profile as Pokemon Showdown! ^.^ The chap who pixelled these little wonders seems to be quite active:
http://www.deviantart.com/art/Pokemon-X-and-Y-Sprite-Dex-364127128
Secondly, I might be able to afford you some assistance with your animations at a later date when I have a bit more free time. I won't be too thrilled to be making any back animations, but if you'd like animations for the more popular pokes I'd definitely sprite some up for you. And until then, I'd like to point you my tutorial for making BW-styled animations without paying a dime for any program:
http://dragondeplatino.deviantart.com/art/Pokemon-BW-Animation-Style-Tutorial-344596875
It puts things down in layman's terms, so I think it'd help those around here who REALLY wants to make an animation, but don't know where to start. It also uses a program called ASEprite which has nice support for transparency, animation and indexed palettes. I'd suggest adding
http://aseprite.org/ and the tutorial to the main post if it seems OK to you.
Anyways, good luck with your spriting project!