Tryzin,
Nice character!
I played with this problem for quite awhile and didn't come up with any truly useful solution.
Some of my exploration went out into different territory because I was trying to replicate your drawing and shapes and that of course only made autoinbetweening associations worse.
A few take aways from my wanderings include...
It may be easier to manipulate some inbetweens via other methods such as skewing a copy of the drawing or using the plastic tool.
I came very close to getting things to work with my version of your character but when I came to the ear... my manipulation required changes to the start or end targets and so tended not to work.
I didn't explore plastic tool manipulation because it was too far afield for your topic.
I am curious if the vector eye pupil and the surrounding white of the eye in your character are two distinct shapes.
It seems to me that wherever OT has to guess how to proceed with an open area (in your case the location where the lines meet to form an oval/ellipse/shape that's the likely place where shapes will deform. I have seen something similar with drawing with the snap feature in that end lines meeting other end lines often don't terminate in compatible bias angles... they meet but with un-smooth deformity (if I had to guess and I do... I'd say the deformity forms toward the side closest to where the origin of the vector line came from).
I'm sorry I don't have any good news for you here.
One thing you could do is isolate those areas to simplify your auto-inbetweening.
auto-inbetween the shapes that are working optimally and then via secondary 'layer' (column/level) resolve the other areas. In the case of eyes and eyebrows (and mouth in cases of lip sync) you'd likely wan those on separate levels anyway).
Combine everything later after getting the desired result.
Knowing more about the specifics of the vector lines you are working with will help developers see exactly what is going on so if you can provide some example files that demonstrate the problem that problem can be further isolated.
So, with apologies for messing with your character... I learned a lot trying to replicate the problem.
Unfortunately not anything that specifically addresses your issue. :(
Hopefully someone else can steer us down the right road.