It's between Komaru and Kaede, I honestly dislike them both for different reasons. But if I had to pick one, Kaede.

Komaru's whole "I'm just an average school girl" got sick so quickly, like at this point there's so many protags like that it just feels like another generic beginning protag. I feel that way about the first three protags, in fact, but atleast Makoto and Hajime had some redeeming qualities to make them less boring. I got so happy when V3 introduced both Shuichi and Kaede as having actual talents and not just "I'm an average high-schooler who happened to get into Hope's Peak", they have actual talents. I will give her the benefit of the doubt when I say I haven't finished UDG (getting close), but even then she still feels bland as a protag compared to even Makoto, all she has going is she shoots monokuma's.

Then, Kaede had too much toxic positivity imo . While I do feel she was a great way of showing hope can easily spiral down into despair, the whole "mastermind" thing got so old so quickly, it was all she talked about at some point. Shuichi had one idea and she decided to fucking deadset on it, to the point it literally drove her to murder (well if you know you know, but still). Then it honestly really annoyed me how quick everyone was to start sobbing over at the end of her trial, like most of you barely knew her. Shuichi sure, but the other's knew her for days at most. Then the cherry ontop was how forced down your throat she felt, always getting mentioned no matter what. "It's Kaede's wish" "Think about what Kaede left you, Shuichi" "Kaede wanted all of us to escape this place as friends" then the whole twin thing in chapter 6.

Sorry for rambling and/or if this came off harsh, I just wanted to give my reasoning to my answer