My two favorites are probably either Lilly or Hanako. Both's scenarios were pretty good (Lilly's good ending... was much more touching than I expected) and Hanako's route always felt a bit "off", but in a good way, as in, "the writers intended it". And I might just be rambling now.
Also, this might just be me, but I have the feeling that all the art in the Lilly and Hanako routes are different from the art in the other routes. For example, I'm getting the feeling that Hisao looks older in the Lilly/Hanako routes, than he does in the Rin and Emi routes.