Personally, I think the difficulty looks something like this:
1. Shizune's easiest. Don't cheat on your girlfriend. This isn't hard to figure out, guys. The only thing that makes this route difficult is resisting the urge to bone Misha... on second thought, maybe that makes it the hardest?

2. Emi's route is very forgiving. You can get to her Good Ending straight from the Dinner Scene, and if you fuck that up, you get another chance!
3. Rin's route, in my opinion, is far less hard than rumored. If you pay attention to her character, the first do-or-die choice isn't that hard to figure out, and if you played your cards right before-hand, you can wind up with two good answers instead of one. Even walking in blind, that gives you a sixy-six point six percent chance of making the right choice. The difficulty in Rin's route is not completing it, but getting to her Act 1 Ending, since that requires you to do almost nothing that indicates you're interested in Lilly or Hanako until the blow-out between Lilly and Shizune.
4. Hanako's route, like Rin's route, has two points at which you can fuck up and miss the Good Ending. Unlike Rin, however, there's only one way to get the first choice right, and the first do-or-die choice comes during a deceptively placid scene. There is nothing threatening in the way Hanako asks, 'What should we do?', but at the point of Rin's first killer choice, the stress is high and it is clear Hisao is in danger of losing Rin.
5. What makes Lilly's route the hardest, to me, besides the fact that you must make THREE correct choices (more than any other route) is the fact that you can screw yourself out of the Good Ending as early Act 2. Don't feel like talking to Lilly about how Hanako relies on her? Congratulations! You're about to go through the next two acts for nothing, then wonder what the hell went wrong.
So you go back to the last choice, the scene in the restaurant, and select the other choice... and STILL get the Bad Ending. If, at this point, you're actually willing to track through every choice you made and try to figure which ones doomed you without using a walk-through, I commend you.
Note: This wasn't MY personal experience, as I got Lilly's Good Ending on the first play-through. I'm still aware of this route's potential to screw you, however.
Your thoughts on which routes are hardest and why?