>>23563335GF are notoriously bad at optimising their games. The DS games had some slowdown despite Pokemon being a relatively simple game and the 3DS games are the same story. The difference between Pokemon and games like Smash Bros and Kid Icarus Uprising is staggering, not only do the latter games run at a solid framerate, they look far better, they have full 3D at all times and they have much more action going on the screen at once.
Admittedly Game Freak had to model all 720 Pokemon and animate them (which would have taken a fair bit of time), but Game Freak were the first developers to get their hands on the 3DS developer kit outside of Nintendo themselves. They had over three years to make X/Y and the end result still feels rushed.