I haven't tried exporting a character with it's control rig because I didn't want to throw all kinds of node garbage to Unity, so instead I used a salve rig that only has the deformable joints.

In my scene with the rig, the actual geometry being shown and deformed is binded to the slave rig to ensure I'm not using a control that doesn't do anything to my character. I then bake the animation to the slave rig, create a character node and export the animation clip.

Then in a GameSkeleton scene which only has the geometry and deformation joints (slave rig), you can import all your animations. You can either put them all in one timeline or as I now prefer, as separate files with the @ naming convention, which Unity reads and splits automatically.

Unity seems to have trouble reading maya versions above 2009, specially with the fbx, you'll want to stick to the 2009 version, which you can choose in the export dialog.

EXTRA TIP: Try using as few joints as you can on your slave rig, though your animation rig can have and probably should have more joints. (for example. you can eliminate the tip joints unless you'll be using locomotion). I also tend to get rid of other root joints like clavicles and sometimes hips on multilegged characters. You can still use them as controls, affecting your slave joints, but without the extra cost.

Hope that helps!

you need to do a bake in the animation... Select all joints/ select all controllers / menu - EDIt - Keys - bake simulation and export with fbx.

i hope to help you.

I am not familiar with exporting on Maya side, but you could try directly importing the maya(.mb/.ma( file into unity. If you haven't seen this already http://unity3d.com/support/documentation/Manual/HOWTO-ImportObjectMaya.html

to get rid to the errors try, edit - delete all by type - non reformer history

That should do the trick. Also on import in unity make sure you have the ik option checked

Oh and also, Maya's fbx is faulty in that if you want to correctly transfer a character, even to motion builder, you need to have your character bound to two root joints, even if the second one isn't weighted.

You can tell in Unity if you select your mesh and if it shows the preview or not. When using two roots, the preview should be there and everything should behave as expected. If not you'll end up having to assign shaders and such to your root joint in the hierarchy which is kind of awkward.