I pretty much think Miyako isn't a good choice for heroine for that reason. Well, partially. The anime, and I assume her route too, expands on why she fell in love with him. I've personally had a similar relationship myself, and that did not work out for reasons that are obvious if you analyse it in any depth. Short version, some things work well to start a relationship, but they completely fail as the base of one.
Chris' first H-scene is very debatable, even in the light of everything else that doesn't follow real world standards. In the best light I can imagine it, she was just too stupid to realise her true feelings, which probably is what they aimed for. How it came out... less bright light.
Wanko's route wasn't really that interesting, with the exception of some scenes, like the whistle towards the end, or the hotel sneak scene (though out of the several similar scenes, I prefer the one where Momoyo caught him, in an oddly touching scene). I see her much more suitable as a little sister character. A fiercly loyal such. In that role I really like her.