Also apparently the reason the 3DS main games lag a lot is because of the models of Pokemon. Rather than downscaling them, apparently GF kept the polygon count, and it's high as fuck (they wanted the models to be used for future games).
I doubt they didn't downscale them at all, that would pretty stupid, as they hold far more data than is relevant for the 3DS' resolution. But the models they used in the game itself still have a pretty high polycount, one of the higher ones I've seen on 3DS.