Weirdly enough, I didn't think the ninjas were that annoying, and that was probably because there weren't many of them each battle because you just have two characters.
I approve of the battle system of this game in theory, but specially in these last few quests I was groaning every time I entered a battle because I knew it was going to take a significant amount of effort to finish, there are so many enemies in each battle and most of them have quite a bit of HP too. It's not difficult (generally) but it takes a while. Having to give full thought and strategy to every single encounter is tiring.
(It would be much worse if those were random battles instead of symbol encounters though, so at least there is that. Though the enemies move so fast you can't really avoid them while also exploring, so dodging the battles isn't really an option.)