Not enough romance between Shizune and Hisao, too much Misha in the latter half of the story, really disappointing ending, etc. It wasn't a bad route just compared to the others it's not as great.
Honestly though, I didn't fully appreciate Shizune's route until I finished her bad ending. The thing about her route is that there's lots of subtle details that a lot of people might miss. The more I thought about it the more I came to the conclusion that there really isn't a "good" ending to her route, it felt more like a neutral and bad ending when it came to Shizune's story.
Personally I would've liked to have seen something along the lines of this for a good ending:
http://pastebin.com/E1cxNLdM