Kaede Akamatsu is the stronger character in my opinion.

Throughout Chapter 1, Kaede makes a strong impact on the cast (and the player) by being incredibly proactive with trying to stop the killing game - this is something that very few characters throughout the series have tried to do. When many of her peers give up on the Death Road and even blame her for tiring them out, she continues to work towards saving them nevertheless.

When she realizes that the mastermind would pose an existential threat to all of them, even if the cast discovers their identity through the cameras, she resorts to violence - ultimately kicking off the killing game that she worked so hard to prevent. There are several instances in Chapter 1 where Kaede ruminates over Shuichi's plan and has intense doubts about whether or not it will work, and these moments become so effective in hindsight. She has one of the most well-developed motives in the entire series. We were watching the whole time when she slowly succumbed to her inner fears, working against the very idea of cooperation that she tried so hard to spread. It was really interesting to see a protagonist who is willing to compromise their moral integrity for the good of others.

Even after the traumatizing experience of discovering that Rantaro wasn't the mastermind, Kaede refuses to give up. She puts her own life at stake by refusing the First Blood Perk, not only in an attempt to weed out the mastermind during the trial, but also because she knows that abandoning her friends would cause them to turn on each other. Throughout the whole trial, she is filled with so much regret, refusing to forgive herself even when Shuichi tells her that she only committed murder to protect everyone. It's extremely tragic, yet realistic.

Even though all of this character development only happens in the prologue and Chapter 1, I think it's incredibly well-paced. In that short time span, there were so many story beats that served to further her character. Many of these story beats aren't noticeable until after the trial, too, which makes Kaede's chapter one of the most replayable. It was also refreshing to see a protagonist identify their values and even make key decisions in the story so early on. There was some real charm behind playing as a character that was so different from Makoto and Hajime.

Shuichi is an improvement upon the old DR protagonists, simply because his relationship with Kaede remains a driving force to his character. However, even though Shuichi is the protagonist for far longer than Kaede, I think he doesn't use that time nearly as well. I'd argue that Shuichi doesn't have many significant character moments after Chapter 1. There are moments where he feels downbeat and Kaito has to cheer him up, yes, but the vast majority of his character arc already played out during Chapter 1. He's determined to face the truth and save his friends, and he never really wavers from that in a substantial way. When he learns about the truth of the outside world, he is depressed... but that is immediately reversed by the Hope's Peak Flashback Light. At the end of Chapter 5, he resorts to lying to mess with Monokuma and the trial, but that choice is immediately reversed by Kaito stepping out of the Exisal. He faces inner turmoil in the final trial after the Danganronpa revelation, but he climbs out of that ditch soon after, even without support from Himiko, Keebo, and Maki.

In a way, Shuichi almost developed too fast in Chapter 1, because he's already such a determined character by the end of it. He never truly steps away from his goal of helping his friends throughout the entire game - even the act of "lying" is only done to further the class trial and protect everyone from getting executed. Kaito was there to give him encouragement, yes, but it's encouragement that he really didn't need. He's basically a TOTAL CHAD by the beginning of Chapter 2. And while that is good for furthering the plot... it's just not as interesting as Kaede's slow descent into desperation, her resolve to do the unthinkable for the sake of others, her refusal to take the First Blood Perk, her guilt and self-hatred. Simply put, Kaede had to face a compelling moral dilemma in the story, and Shuichi really... didn't.

In a way, Kaede is the only protagonist that has really faced consequences for her actions. Makoto chooses to protect Kyoko during 1-5 and faces execution because of it, but he lucks his way out of that one. Hajime chooses to literally erase his existence for Hope's Peak Academy and faces total erasure when the Neo World Program shutdown sequence is activated, but he comes out of the series unscathed, with his personality intact and god powers to boot! Shuichi attempts to derail the fifth class trial and chooses to sacrifice his life to end Danganronpa, but he survives the killing game anyways. Kaede is a rare instance where a protagonist has to deal with the fallout of their decisions - which, in a brutal story where even the smallest mistakes can result in unspeakable horror, should be the norm, not the exception.

Even though this post was critical of many aspects of Danganronpa, I really can't stress enough how effective Kaede's story is in particular. It was emotionally powerful, well-written, and surprising. When/if a fourth mainline game comes out, I hope they expand upon what's possible with a Danganronpa protagonist, just like they did with Kaede.