The training trio is the emotional core of Danganronpa V3, and I think that does fascinating things for the game's structure. Makoto and Hajime had characters they felt closer to than others, but they didn’t really have close friends in the way Shuichi does. It's an interesting change of pace to have such a close group at the heart of a Danganronpa game.
I found this shaping my decisions as I played Danganronpa V3. In the first two games, I went, 'Who do I spend my free time with? The characters I like, I suppose.' In this game, I went, 'Who do I spend my free time with? Well, I think Shuichi wants to hang out with Kaito and Maki, so that's what I'll do.'
I'm particularly interested in Shuichi's dynamic with Kaito, because... well. Well, because Shuichi is catastrophically in love with Kaito. It's the only way I find myself able to interpret their relationship.
Shuichi: (Kaito is always so honest and approachable. He’s willing to help you with anything.
...Only someone like Kaito could help me.
Only someone like him could tell me what I need to hear.
...Ah, n-never mind. I shouldn’t be talking about another boy like that...)
The moment I saw this internal monologue in Kaito's fourth free time event, I was doomed. Maybe some people are capable of seeing those lines and walking away unconvinced that Shuichi is in love! I am not one of those people.
When Shuichi and Maki first started training together without Kaito, I thought 'wait, are they going to set up a Shuichi/Maki romance?' and, nope, it was just an excuse for Shuichi to talk to someone else about how in love with Kaito he is.
Shuichi: Overthinking things and worrying about what I need to do... When I’m with Kaito, I feel like... all of that stuff just fades away.
Maki: Do you... look up to that idiot?
Shuichi: Ah, I don’t know if I’d call it ‘looking up’ to him...
'Kaito... you really are something else,' Shuichi says aloud to himself at one point, lying on his bed, alone in his room, because he's not in love. In Kaito's Love Hotel scene, Kaito pins Shuichi against the wall, and Shuichi cannot handle the sexual tension:
Shuichi: (I barely managed to meet his gaze. He felt so close, looking down at me... that's when I remembered where I was, and...)
Shuichi: Ah, Kaito! Ah, b-back up a little.
Shuichi: (My eyes darted around the room, focusing on that weird bed behind him... I was so caught up in the fantasy that I forgot where I was for a minute. But with Kaito so close to me, in a place like this... It's hard to stay calm.)
I'm not saying you have to agree with me! I'm just saying that I'm right.
I've contemplated how Shuichi and Kaito would react if they had to stay overnight in a place that only had one bed. (If you've looked through a lot of this website, you may have noticed that 'only one bed' is very much a recurring theme.) My answer: Kaito talks very loudly about how they're ONLY SHARING A BED OUT OF NECESSITY, NO HOMO. Shuichi is trying very, very hard to ignore the intense and building feelings in his chest.