She is hard to use, but I think the problem is that she's too much of a generalist without having the real utility that Lee Sin has.
Her human form spells can be powerful, but scale only off AP. Her W can do a lot of damage, but only if she is all AP. Her Q is an initiate as it does % current Health damage so it can't kill, but it can tear chunks off healthy tanks or champs. Her E is her only stun and it is a skill shot.
Her Spider form is a melee assassin with her W giving her an attack speed buff and her Q being a % missing health execute. These don't scale well off AP and don't do a lot of damage to anyone who is healthy.
The problem is that unlike Nidalee who gets great damage on her human Q before transforming and going in for the kill. Elise often has to take multiple shots before she has someone damaged enough that she can dive in. The synergy just isn't there.
She also lacks the mobility of Lee Sin or Nidalee.
I like the spider queen, but just take her into a couple of ARAMs and you quickly figure out just how broken her kit is, but in the wrong way. She can't really hurt anyone who is healthy. Her assassination tricks require her to all-in while in spider form and her rappel is a lousy escape when you don't have an enemy minion or jungle monster available to jump to once you are up in the air.
Someone who has mastered her can probably make her work, but as so many other posters have said. The rewards are low for the effort.