Sorry I missed this question. Was intending to put it off because I wanted to give a proper reply, which would have taken some time to write...
Favorite route... God, it's been a long time. I think I really liked Kotomi's route. She has the best ending of all. Fuko's route comes close due to the feels-factor. lol Maybe Nagisa's main "After Story" route would be third due to all the little things I liked about it (the realism, the spotlight on a young adult working his butt off for his kid, Ushio, etc.).
Honestly, I can't really remember. I mean, my favorite girl in there is either Fuko or Kyou (Tomoyo is a very close third choice), but I can't remember much of Kyou's route more than I could remember Kotomi's route (probably due to how distinct Kotomi's ending was). Like I said, it's been a long time.
Sorry if my answer isn't satisfactory. My memory sucks.