First of all, I don’t find anything wrong with someone (ANY GENDER) wanting to look pret...

First of all, I don’t find anything wrong with someone (ANY GENDER) wanting to look pretty/handsome/whatever for the person they like. This is a human thing, not a gender thing. I just think the translation/writing didn’t convey this idea very well. Because even though Ito gets embarrassed by wearing dresses/skirts/etc. she doesn’t hate it per se. It’s just inconvenient for her because she’s so energetic and ends up, somehow, in fights or instances where she moves a lot.

I.Psychological Reason
II.Appearance Reason
III.Makoto

When she was young, her dad (and brothers?) said that she couldn’t learn martial arts because she was a girl. Jota used to bully her because she wasn’t acting like other girls and wouldn’t cry (also he liked her but this is from Ito’s pov). So Ito started hating being called a girl because it was restricting her. So Ito took matters into her own hands and decided to stop looking like a girl. The thing is, she’s still a girl? It really wouldn’t change anything, realistically. She doesn’t deny that she’s a girl; she still identifies as a female. I think she correlates girl=weak and guy=strong (in terms of being able to do things). Ito doesn’t hate other girls and doesn’t look down on them if they’re cute or trying to be cute. I don’t think she thinks it’s possible for her (personally) to look like a girl and still be able to do things other boys can do.
Throughout the series, Ito doesn’t think she’s pretty or good-looking. She said at one point in the beginning that she didn’t look good in her uniform because she’s so tall. I relate to this because I’m tall and I have an older brother which people constantly say we look like each other. I always think, “Are they saying I look like a boy?” It’s kind of weird to think like that because I know that’s not what they’re saying. But it still lowers my self-confidence for a while. Ito has self-confidence issues as well. She thinks it doesn’t suit her and kind of embraces it by going the other way: dressing like a boy. There are instances where she gets grumpy when someone who knows she’s a girl says she’s not feminine. It irks her because she knows (or thinks) the same thing. She doesn’t have the self-confidence to dress like a girl and she never dealt with this issue. She started avoiding it.
So Makoto. He always compliments her, no matter what she’s wearing. He loves her because of who she is instead of what she looks like. This doesn’t mean that he isn’t stupefied when she surprises him when she starts dressing differently (drama princess costumes). He thinks she’s beautiful. Again this isn’t a gender thing; we all get surprised when the person we like dresses nicely/differently than usual. I think his compliments really helped Ito gain self-confidence because she said it herself, no other boy had called her cute before. Also he knows that she can handle herself in a fight or whatever (rescuing Akane etc.). He doesn’t restrict her. The whole he not wanting her to be alone with Toki isn’t him restricting her but him wanting her to be careful. Men are stronger psychically than women (as annoying as that is) and Toki is a lot bigger than Ito so she wouldn’t be able to fight back (Ferris wheel incident). Makoto doesn’t want her to ever go through that again so he’s protective. I think because of him, she realized that she could be wearing high heels and be able to kick ass also that she’s beautiful.
Also the most important thing (to me that is) is that they don’t care that the other dresses in the opposite gender.