this happened;
Undesirable, clearly
The playermesh pops out of position to the exact same point regardless of how far the hips translate in the animation
How do I rectify this?
I think I’ve solved this problem, under the animation import and root transform position (Y) I checked Bake into pose, based upon original and offset it until the character’s feet line up with the ground, I guess that disables Mecanim’s interpretation of the root
Having a new problem but decided against creating a new thread, so I just cut down the original post and left the solution
I’m much further in the process of getting my animations ingame now, but the Mecanim system is still fiddling with my curves
I’m copying my Maya binary file straight into the project files and ticking ‘Bake animation’ which is working much better than the FBX method, but the hips, spine and chest joints look too stiff;
Playblast from Maya (right click and loop)
Animation ingame
It’s subtle, but watch both side to side and you can tell the chest isn’t rotating side to side as the robot throws his arms out (shown more clearly with the camera top down)
Additionally, I set up an FK/IK blend and as a result used IK for the legs in my walk animation (not shown in the above video) and the right foot is fine but the left is bent at a considerable angle throughout the loop
Comparatively I used FK with the jog animation and it turned out fine, no weird angles
I have to ask again, what is the correct way to set up a rig/skeletal hierarchy so that spinal and hip animations are supported? I’ve rigged to the Unity recommendation in the docs (my Hips bone is considered the root)
Come to think of it I did get errors in the console when I imported the animations actually, something about “this joint between human transforms has translations which is not supported”.
I received that error once I think it was for a bone that was accidentally scaled.
I believe your avatar needs to be ‘tightened’ up. Several adjustments could be made to the areas you listed as problem areas chest/ankle.
I use Max but I’ve found if the rig setup in Unity (mecanim) is done correctly none of these problems exist or are easily fixed through the setup process. And from experience and testing Unity does not fiddle with animation curves when exporting/importing using .fbx.
The ankle problem is odd - I haven’t encountered this issue so I can’t comment on it. I use Unity free at this time.
Cool fan/motor components on your characters back! Did you use blend shapes for those?
For rigging Unity/Mecanim humanoid ready models- check out Mixamo’s autorigger- it creates perfect Mecanim rigs every time- You can only use it once per email account without paying though- wish they would sell it as a standalone app-
Then if you want to also animate by hand- bring the rigged model into your 3d program and add controls- that way you have a rig you know works with mecanim and you can create custom animations-
Yeah I went back and redid the rig, last time I had like 5 spine bones, a double foot bone for each foot, and a wrist bone in between the lowerarm and hand bone which was just too much to handle for Unity
Mecanim seems to like this skeleton a lot more which is good, no greyed out or redundant bones
My theory is that Unity couldn’t use 3 of the 5 spine bones which removed their cumulative rotation of the spine (each segment only rotated a few degrees) and got confused with the feet as I had two bones as the same foot bone which I hope I have improved upon with the new skeleton (though after animation tests only the big toe appears to animate 
bummer) - I hope the spine rotation works when I do some new animations
The spinning objects on the back were just added as separate meshes and each are parented to empty Gameobjects which are in turn parented under the chest bone. The empty objects are scripted to spin via local rotation at different speeds and can be translated forwards so that they go inside the torso for the effect I want, I haven’t learnt blend shapes yet, I thought they were only for facial animation! interesting, I should look into that
Come to think of it the character is basically made up of lots of separate meshes which are individually smooth skin bound to their respective bones rather than one big mesh, so I wonder if i’ll get more errors than usual doing something so unconventional
That is what i’m doing! It is tempting to use an autorigger or an already made rig but it’s more impressive on my portfolio if I do everything from scratch, even if I do get showered with problems
I suppose that just means I learn more
Your skeleton looks a lot more manageable and closer to what Unity likes! That was definitely the problem you were having.
I also had about a week where I was trying to force a 3 spine rig into humanoid form. I wish Unity would give us 3 spine bones. I don’t agree with there justification about the 2 spine bones but gotta make due with what they give us. I’m not complaining 
just would like 2 diaphragm bones and one chest bone - or one diaphragm bone, one lower chest bone and one upper chest bone.
Ah! Good setup for the back objects. That’s how I would do it as well.
Yeah blend shapes/morphs can be used for a lot of different applications but most people only think of facial animations (which is one of the best applications for morphs).
Keep in mind a morphs can be used in place of bone animations (especially good for creating a scaling effect which Unity can handle but doesn’t like too much).
I don’t think your character setup with multiple meshes is bad. This setup is common - and one of many ways to do multiple outfits/loadouts for a customizable character setup.
Your mesh is pretty dense in some spots but I don’t think it’s terrible. Nice problem solving! Keep it up.