We don't know if Thainendra want to purge all humans or only the currupted ones (still probably billions).
On the good side Thainendra seems to have honor, is forthcoming with information and is honest what his plans are.
For Zel, beside her eugenic experiments, she has zero morality, lies/manipulate everyone, uses terror tactics and bombing, she doesn't care for human lives (on the contrary she encurages the MC for the more extreme options nearly every time) and even actively trys to corrupt him with dark light one time...
I think while extrem in short term, Thainendra's path will be better for humanity in long term, as in a 'better' humanity.
Zel path seems better in short term (no billions of death), but in long term i think that ends far worse for the humans...i imagine her paradise will look similiar to Slaanesh (wh40k), at least thats what i get from her character so far.
As such i would say Thainendra is the lesser evil.
Or in a more eloquent way
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James, it is said that corruption is like a tree. You can prune away its branches, even cut the tree to the ground, but it will grow again ever stronger. Such is the nature of corruption and why it is so difficult to destroy. Some may question my right to kill billion of souls, but those who truly understand realize that I have no right to let them live.
No sacrifice is to great.
No treachery to small.
Thainendra protects
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