To me, the best route of S is... the common route.
I enjoyed discovering Benkei, Yoshitsune and a bit of Seiso.
Kokoro, Margit and Tatsuko were nothing more than sex fanservice in my opinion.
The beginning of Tsubame route was cool, until the tournament.
Mon-sama's was well developed storywise, but I'm not too fond of lolis.
And finally, I was a bit disappointed in Koyuki's,