Hints or not don't change the fact he was kind of a dick because she didn't want to sleep with him, and I don't see him as the sane one of the group, he's more like the ignorant one and disposable one, besides to show how Yuma loves Hotaru but doesn't see that yet he didn't really have any importance to the story, so much that even you said he should be left out of the picture already.
And sorry to say but you don't know me then, I admit that I am a little biased because of yuri, of course I will favor yuri relationship over others, but that doesn't mean I'm biased like the yuri fans you mean, I always try to not be biased like that, I don't think Takeda is annoying because he's "nice", although he is better than the others I don't really find him that much nice either, I just don't see being nice as a reason to like anyone, to me that feels like harem bullshit where the protagonist is a bland idiot whos only quality is being nice and all girls fall in love with him only because of that, if I find him annoying it's because he's an idiot who pretty much could have disappeared from the story and wouldn't be a loss at all.
But I do get why you thought I'm like that, I also don't like how some of yuri fans treat male characters in yuri, especially because some really don't deserve it, the problem is that a lot of times they really are made to be that bad, like pushy borderline rapist or super jerk rapist like Fujiwara, unfortunately yuri in general lacks good male characters, but most yuri tend to focus only on the main characters and give a little screen time to people close to them, so it's not like male characters are really necessary even if they're good.