Iv'e noticed that whenever I'm in a fight with trolls (usually the 2 weak ones and 1 strong one), the animation gets really choppy and slow, but all other fights are fine.
It's not an issue with too many units in the battle, because right after once of these choppy troll scuffles, I had 2 battles in a row against a dragon and some pack drakes with 2 similarly sized forces. The first force took care of the little drakes. The second was actually my main army that I used to defeat the trolls (slowly).
Edit: I also want to add that I just started playing FE today and it's really fun.