Koishi, without a doubt.
Yukari may be one of my favorite characters, but Koishi's boss battle is just so much better designed. Most importantly, the difficulty. Yukari was a joke, but Koishi was actually moderately challenging (I think it took me ~8-10 attempts to beat her the first time, and I haven't yet done a one-miss clear like with Yukari and Suwako).
Her theme song is better, and she's a more amusing character.
Finally, HER HAT. I don't know why I love that damn hat so much. I really want to bring it into Team Fortress 2 and put it (and the closed third eye) onto the Spy. Speaking of which, Koishi makes an excellent Spy (and I wonder
what's for dinner how a Fancy Fedora would look on Koishi)
But other than that, I think Nue's pretty good gameplay-wise. I was tempted to say Koishi, but her fight gets boring once you memorize everything. When it comes to Nue, I could know exactly what I need to do, but she can still get the better of me every so often. :derp:
After getting accustomed to the attack patterns of both, I'd still have to say that I find Koishi harder.
On the other hand, I'd like to play against Koishi again, but DAMN the stage is SO BORING. In contrast, Nue's stage is much more interesting (and legitimately challenging), none of this obnoxiously slow bullet ring BS, instead you get some awesome arcade-style bullet hell patterns.
Well since everyone else is saying gameplay...
Nue's the most fun for me, with GFW Marisa in second. Most of these bosses are pretty dull to fight once you get the hang of them, probobly due to the unreasonable number of non-random attacks they always have.
True that. I think all the Extra Bosses could use faster-paced and shorter battles with more randomized attacks.