Animation and rigging Pipeline/Workflow Advice

I am a Unity noob and now I have taken a new job as a CG artist. I convinced the new company that Unity was the way go versus the old builds in other engines and now I have "promoted" to technical director. I have some great resources, but I really want to set up a solid organizational pipleline. We were able to nail down asset creation/conversion very easily thanks to Unity. My questions relate to the fact that I need to find the best modular way to deal with rigging and animation imports. Basically 3DS Max exports one read only animation data file. Also, any more complex scripted/IK/customized controller type rigs lose most of there functionality in Untiy. Combined with the fact that Motion builder does not like none human rigs this is getting tricky. Our products have complex hydraulic rigs, creatures of all sorts and vehicles. Is there any way to have an animator just writing and exporting animations as stand alone files from Max/Maya? Or do we have to rig everything in Unity using only fk and custom scripts or always be importing entire FBX files?