I think the biggest problem with most of the 3D model sprites is how many of them are not moving at all.
I really enjoyed how the sprites helped bring life to the battle doing their unique little motions. So many pokemon in XY/ORAS just stand completely still, you almost start to worry that they died standing up on the battlefield.
My second complaint is the sizes. As
>>22630530 points out, Wailord should not be that small. I know why he is that small I guess. Im assuming its so the 3DS can handle it and so you can actually see the battle on your tiny screen instead of a giant blue blob. But it just takes all the fun out of raising one up. My second complaint is it ruins how I saw certain mons. Back in fifth gen, I loved Excadrill, it looked so fucking bad ass. I didnt even realize it was so small until later on, but the sprites made him look intimidating as hell. But in 3D it suffers from being small, looking a lot less bulky then I thought it would, and once again, he just sorta stands still all the time.