I completely agree that the Crab have their downsides, after all, all of the Great Clans of Rokugan have some Serious Skeeve going on, which more often than not revolves around thinking their own particular way is the best way.
The Crab have been forced to become like the monsters they face and devalue everyone else for not suffering as they have, the Lion are so arrogant that Bellerophon would suggest they tone it down, the Crane are Form over Funtion to the point of insanity, the Phoneix are ruled by arrogant Mad Magicians, the Dragon can't speak clearly to save their lives (other than the Kitsuki who use...EVIDENCE instead of trusting the honorable word of samurai), the Unicorn are just kinda foreign to Rokugan and have the same sort of combat arrogance the Lion and the Crab do, and the Scorpion's only redeeming value is their near absolute loyalty!
In general, they've all got stuff that makes them seriously disliked by different groups in the fandom and within the setting. I think the Crane get a lot of Fandom hate because their whole thing is very classically Asian. It rubs people the wrong way because it's a somewhat alien mindset. I personally dislike the Crane because of their whole Arrogant Superiority thing. They can be every bit as underhanded as the Scorpion in their manipulations, they just do it in a way that is socially acceptable because they control what society finds acceptable. Plus, they don't have the whole Loyalty thing the Scorpion have.
Personally, my favorite clan is the Dragon, but I can admit that dear god they are far from unblemished paragons of righteousness. The thousand years of more or less total isolation and Hitomi's entire reign spring to mind.
Also,
@storybookknight, Good Point on the Dragon Lion alliance being remarkable. I had completely forgotten about the Dragonfly thing. Though, I think that the rivalry there was mostly sublimated from the Dragon to the Dragonfly. Honestly, I'm not 100% on why the Dragonfly even GOT to be a Minor Clan though given the whole Love is a Curse thing in Rokugan...