It was the combination of nerfs to her Q damage, the removal of Deathfire Grasp, and the mana regeneration changes that pushed her out of the meta.
I believe she had some changes made to her E regarding the collision detection of the balls, though I can't remember if they served as a nerf or a buff at the moment.
Also, pre-5.5, aggressive dive-oriented junglers such as Vi and Jarvan were popular, which an immobile mage such as Syndra doesn't fair well against.
She's still a viable pick at most levels of play if you are good with her.