I'm writing a full-fledged team builder that will be a component of Technical Machine (but will also just be a stand-alone application). My plan is for it to generate a team based on a few criteria, but also assist in making changes. In other words, you could build your team with it, filling in as much detail as you like, and Technical Machine would then fill in the rest for you. I'm even thinking about stuff like "What effect would changing this EV spread to that EV spread have?" and it would calculate change in physical / special defensiveness.
I have some stats that I would be interested in and would begin using immediately:
Taking into account EVs, nature, and item, what is the exact Speed each Pokemon has? One thing that would be especially useful is an evidence-based approach to Speed. If there are no Pokemon that sit at 237 or 238, then there is no point in me EVing a Pokemon to 238. I want to be able to do something like "For X more EVs, I can outspeed Y% more Pokemon.". I would probably also make some sort of graph showing Speed distribution and post that, so people can see it visually. Perhaps my program could include the graph and display your location on the curve, along with a percentile.
Move set stats that parallel team mate stats. If I have statistics like "On Pikachu, 29% of Pokemon with Thunderbolt also have Surf. 23% have Hidden Power. 13% have Quick Attack.". From that, I could construct a complete move set given any partial set of moves, just as I do for Pokemon prediction. Of course, more "complete" stats would be "Given that I have seen a Pikachu with Thunderbolt on a team with Geodude with Tackle, 28% of Pikachu also have Surf.", but I imagine that those stats would be much, much larger.