So a few days ago I decided to play through this. My first time, I got Emi's good ending. I don't know if that means I'm good at decision making or I just got lucky. Probably lucky, I got the Act 1 bad ending the next two times after. Following which I looked up a walkthrough for the rest of the routes.
So far I've gone through Emi's, Shizune's, Lilly's, and Hanako's routes, in that order. So far, Emi's is my favorite, with Lilly at second. Lilly's WOULD be my favorite, if not for being so heartrending (I actually cried for a little bit

). Funnily enough, I never expected Lilly to be an option on my first playthrough. I don't know why, I guess I thought Misha and Shizune would have separate paths, but nope. The closest you get to a Misha route is Shizune's bad ending.
Speaking of Shizune, her route is okay. Not because of the fact that she's deaf, that has nothing to do with it. It just... doesn't seem as good. Probably because there's not as much "romance" as the others.
Hanako's is my least favorite for two reasons. And no, it's not because of her scarring. One, there's not a lot of romance, less than Shizune's route even. Two, it ends pretty abruptly.
I haven't gone through Rin's route yet, nor most of the bad/neutral endings. I don't have the heart to, I guess, especially after how heartrending Lilly's good ending is.
And yes, I realize this is a one-year bump, but I felt like I should explain my experience with the game.EDIT: Changing my favorites a bit. Shizune's is my least favorite now, with Hanako being third, Lilly second, and Emi first. I'll update again when I go through Rin's.