To be honest, virtually the only thing I didn't think cliched was the animals spirits part. I've not come across that a great deal in the novels I've read so I don't know if it is in fact a common trope, but if it is, then it may well be the easiest to subvert eg by looking at the animals in a different light or how they affect the protagonist. For instance in his series Shadows of the Apt, Adrian Tchaikovsky gives the people insect characteristics, whereas in his Echoes of the Fall the people have the ability to shapeshift into specific animals and they build communities/tribes around that ability -- so two sets of novels by the same person both dealing with animal spirits/characteristics, but how they're handled is very different.
For me, the evil teacher/superior who is cruel and abusive simply because he's evil is as trope-ish as the kind mentor who helps out simply because he's good -- no one is entirely bad or entirely angelic -- and I do fear they run the risk of being seen as cardboard characters. Much the same applies to the evil Big Pharma corporation. The MC's character arc is similarly somewhat hackneyed to my mind notwithstanding that it's based on a true story.
But I do think that rather than spend more time worrying about the plot at this stage, you might be better off actually getting down to writing the story. See how it develops and then when you've done stand back, get some feedback from a writing group, and examine what works and what doesn't.