@zeffiez
The "Thus Yu Ishigami Closed His Eyes", arc covers his past. Specifically, it makes emphasis on his habit of doing nice things in secret without wanting compensation (chapters 80, 88), and the consequences of such acts (55 and 88 again) Such actions aren't portrayed as good or bad, but as immature, being the root of his own suffering, regardless of the outcome. Would Miko antagonize Ishigami so much if he had openly supported her in middle school instead of writing an anonymous letter? Would he have been suspended had he shown the evidence to Kyouko Ootomo instead of facing her boyfriend like some sort of protector in the dark? Probably not. And it's immaturity because while Ishigami does attribute his acts to nobility, they also show an unwillingness to compromise in his beliefs and a fear of standing in the spotlight. As cringy as his ideas to woo Tsubame were, they were also indirect as hell, showing that he's still unwilling to take responsibility for his own feelings. He's afraid, and who can blame him after what he went through. I think that's Ishigami's main issue and what "closing his eyes" refers to. Not being afraid of facing others, but of facing the effect that his own actions have in other people, be it good or bad. That's why he didn't notice Tsubame's reaction to his "confession".
And what does it have to do with his romantic prospects?. On one hand we have Tsubame. Open minded, beautiful, smart, cheerful and somehow still single, which makes her a very enticing target for a boy his age. She was also the first one outside of his circle of SC friends that openly supported him. An inverse case of what many harem haters like to say, "he fell for her because she was nice". And that's exactly the problem with her. His feelings for her are shallow, since he doesn't know her besides that. An argument may be made that Kaguya's feelings for Shirogane also have their roots in him being nice, but the circumstances are completely different, since Ice Princess Kaguya, out of paranoia, took her time to know everything about him down to his birth weight and was won over slowly. There's also the fact that he has needed support in order to improve himself and try to confess. Which by itself would be fine and dandy, but the problem lies that his motivation for pushing forward wasn't his love for her, but his resolve to not disappoint Kaguya. There's where the "closed eyes" come to play. Except for the "confession" every action Ishigami has done regarding Tsubame was to appeal to her. He never tried to open his eyes and see the person in front of him. She's as distant as an idol to him.
Regarding Miko things change a lot. For better or for worse, her existence is something that Ishigami simply can't ignore. Even if hostile, she has forced him to look directly at her, thus he has been forced to learn about both her good and bad sides. He recognizes her naivete, which in a weird way mirrors his own immaturity, and unlike with Tsubame, he faces her, even if what he says only ends up angering her. They don't get along precisely because they have actually bothered to learn about each other. Miko can't completely lash out against him because she knows what he has been through. She knows him enough to trust that he's not a stalker, despite very incriminatory evidence. And he can't help but be worried about her because he knows how straightforward and stubborn she is. There's also a bit of gratitude there for openly facing him while the rest of his classmates avoided and badmouthed him behind his back. Their relationship makes a better parallel to Shirogane and Kaguya, hostile due being apparently incompatible, yet there's that spark of brilliance in both Kaguya and Miko that both Shirogane and Ishigami can't help but admire.
Does that mean Miko is Ishigami's endgame? Hell yes. Does that mean his confession to Tsubame is doomed? Not really. Even if based in a misunderstanding, Ishigami also has Tsubame's attention, for very similar reasons. He did something that nobody else did. She's rather curious as well, so they may start dating at some point in time, but it likely won't last long. On the other hand Miko's character is still underdeveloped. That shows in her lack of interactions with the second years in the SC despite being a member herself. She's also immature, but for very different reasons to Ishigami, which at least would be a couple of paragraphs more so I won't delve into it. That Kobachi is finally letting go of her hand means that it's finally her turn in the spotlight. Miko arc is coming, and after that we'll see how things develop, but all evidence points to her realizing Ishigami was her flower prince all along. It's hard to tell if this will solve organically or devolve into the usual harem bloodbath, but let's have faith in Aka.
P.D. To those who ship him with Onodera, unless we get more material to work with, she's the equivalent of that girl who sat besides you by pure coincidence and now you can't help but wonder if she likes you. To those who still ship him with Fujiwara or Hayasaka... let's give up... okay?