I played Tonoko's route first of the three the first time I played the game. Admittedly, the route is slower-paced than either Miyabi or Shino's routes, but it has its own charm. On my second playthrough I found Shino's route to be the best of the three, a route that got tastier on the second playthrough. Miyabi's is a good route no matter how many times you play it. Playing Tonoko's route the second time was not as good as the first, but it was still a good experience.
The route that I had the most trouble playing the second time was Yuuna's, because all the shocking revelations were already over with. It's the kind of route that is godly the first time you play it, but has little to offer on a second playthrough, in my opinion.