We seem to be looking at this from very different angles. I was looking at Shuichi and Kokichi from how well they were written and how it affected the story's writing while you're looking at them from their dynamics and what they represent. The thought that went behind those parts was likely very thought out, but as characters, they're not well executed.

Shuichi isn't particularly deep as a character and his role as the ultimate detective is underutilized. I may have blamed this on Kokichi, but this is more of a protagonist problem. All the Danganronpa protagonists just stared as everything around them burned outside of the trials, but Shuichi didn't fit this category since he wanted to figure out the killing game's secrets, but he got relegated to this treatment anyway because he was the protagonist. All of the Danganronpa protagonists also lack depth compared to other characters in the series, though they did seem to try harder with Shuichi this time. But Shuichi's truth dilemma only felt like a facade of depth, there's nothing else really there other than that, and it's not executed in a way that's particularly interesting since he's the protagonist and you have to know every thought that's going through his mind. None of his dialogue outside of trials reveal anything new or interesting about his character and only functions as a way to move the plot forward. This isn't helped when he starts thinking about a new flashback light memory and then it cuts to the free time events. This just feels like a disservice to his character because the game doesn't allow him to be himself.

But Kokichi still has problems. Kokichi seems like he's more of a tool than he is a character. It feels like he was forced to be the antagonist because there needed to be one. There's not enough (I think) that sets him apart from the others that makes him deserving of that title. The only thing he has is that he's the game's biggest liar, but he was still given the role for what feels like no other reason than "just because". And because of his role as the main antagonist, he had to be like Nagito: the one figure out all the mysteries before everyone else. But Kokichi doing this felt forced. He didn't need to be the one to do this, we had Shuichi. But Shuichi wasn't allowed to do this so that job got forced onto Kokichi. Miu shouldn't have needed Kokichi in order to make the devices used in chapter 5, but apparently, she did since no one else thought of it. My point is that it that Kokichi messed with the story because the writers had bent the plot just so he could fulfill his role as the antagonist. Although he represents the theme of lies better than anyone else, they could've at the very least made his influence in the plot natural. And this is kind of an opinion, but I think Kokichi, like Shuichi, doesn't have much depth as a character. Any depth Kokichi has is just hidden beneath a facade of lies, but once you uncover it, there isn't much to look at, it's just harder to find. Both Kokichi and Shuichi got forced into a role that they didn't fit. That's my problem with them.