Annihilation is not complicated at all, the whole thing is just a metaphor for various traumas and how we deal with them.
Natalie Portman and the guy go through the trauma of infidelity within marriage, they both come out changed by it, different yet the same, hence the shimmer in their eyes at the end.
The first scientist chick who dies to the bear, she lost her daughter to cancer, completely out of her control, just like hear death to the bear.
The chick that ties them up, she is an ex addict, she dies to self-destruction, the actions she takes directly lead to her death by the bear, just like an addict their own lives.
The chick who plays Valkyrie in Thor, she suffers from depression and self-harming she dies by giving up.
The main scientist lady, she is dealing with cancer too and her own body betraying and destroying her.
There is a reason they talk about the still alive cancer cells from a 100 years ago at the beginning too.