Probably level 13: Dancing Floors. It's an enjoyable stage and it has my favorite track from Turquoise October.
Least favorite is definitely the Experimentorium (sorry if I butchered the name). It's probably the most tedious level by far.
Also, I agree the final boss was really bad. From a cinematic standpoint, it's great. But from a gameplay standpoint, it seems to me like they had something better planned but were short on time. Definitely a disappointment considering Splatoon 1 had such a good final boss.