I've been able to export FBX animations from Maya LT 2016 into Unity to use with Vuforia without problems if I make the animations "Legacy" within Unity.
I would like to use the default, "generic" rig in Unity so I can use Unity's Animator. Any tips on how to do that? If I don't select "Legacy" and use the default "Generic" within Unity, I am getting an issue of slow Vuforia recognition. The AR target is found but the animation plays BEFORE showing up 3D model even shows up on the screen, the net effect is when the animated 3D model appears over the AR target, it has already reached its last frame without showing any of its preceding frames. Those problems go away if "Legacy" is selected, but then I lose the use of Unity's Mecanim controls.
I am using Vuforia 5.5.9 and Unity 5.3.2f1 on a Mac.