I would like to see a legendary that has an evolutionary line. I know that seems like it would make it less legendary, but it could be good.
Also, why not have EV's and IV's actually show up? What's the point in making you keep track of them outside of the game?
One thing that would be interesting but I doubt they would do, is make the professor in the game a trainer too. Make it so you beat the Elite 4 and go through some other things, and then he reveals to you that he used to be the champion, but he retired because nobody could beat him. Then he battles you, and his AI is the best in the game. Get a bunch of competitive battlers to work on it so he's top notch, that way you actually have something really challenging at the end of the game.