Not being able to farm efficiently is the same thing as falling behind. Counter jungling is an issue, because Shen cannot out-duel most junglers. Sure, he will not die to his enemy counter jungling him, but he will not be able to contest his already slowly farmed jungle. Also, a 1.5 second taunt on a long cooldown is not a considerable form of cc. For example, Sejuani brings a knock up w/ gap closer, a near perma slow, and a root. All of that has much, much more burst damage than Shen, too.
Shen does not bring the damage nor cc that a jungler needs. What makes him a viable jungler is his sustain and global presence, two things that most junglers do not have. Shen trades damage and cc for this, which upsets overall team composition in the meta. A team composition would have to be tailored to him, which is why he does not see much play.