There are? If so, I agree it is a neat touch. For some reason I'm reminded of Secret of Mana where as your magic levelled up, so did its animation (and, in the endgame, spells levelled up beyond Lv.8 got extra-special animations).
Yep, according to the official English site, Pokemon played with using the Pokemon-amie system will have special cosmetic animations and actions in battle, such as looking at you for advice.