I kinda like the over complicated systems they designed, its a sign of hubris and a flaw in a lot of modern design. They thought they could control everything and got fancy with designing a reset system in HADES etc.
They could have printed out a good survival guide as a backup and stored it where the new humans are created as a backup.
I think HADES and the complicated approach made sense in terms of Hubris if they didn't have Elizabet so clearly defined. HADES is something Ted would have considered for inclusion not her...
To be fair though, GAIA did work as intended for 1,000 years, minus APOLLO, obviously. And the trouble started because of an outside signal, something they never could have predicted when they were designing the system. I mean, the alternative to building HADES was either program GAIA herself so that she's ok with destroying life in certain circumstances, which would present it's own giant host of problems, or take the chance that if GAIA messes up, then it's all over, she'll just spend the whole time trying to correct a fatally flawed biosphere and the whole project will fail. HADES sucked, but was totally necessary.
Yeah if I take the context at face value I always come to the conclusion that Elizabet would have given the decision to GAIA to decide not a separate sub-routine.
If you think about it HADES is too close to ME3 logic - "to save the world from a plague of biomass consiming machines we've programmed a machine to destroy the world with a plague of biosmass machines!"
Also to be blunt HADES logic would make sense if there was reason to believe conditions on Earth would be hugely different or if they were terraforming another planet.
It's reseeing the same soil and ecosystem as before so the odds of GAIA getting it wrong given she's not creating new organics but merely recreating organics known to function perfectly well (grass, corn, etc) should have been pretty low.
That said they did give a decent logical explanation for HADES and like I say the idea was ultimately more driven by narrative need than character consistency so It's not a huge biggie: HADES makes for a nice threat.
Going forward though I will tire of the franchise if they keep trying to re-do Zero Dawn with constant threat of biomass consuming machines. That's been done twice now already - once as backstory and once as the "big bad" for Aloy to defeat this time around.
They need a new direction for future antagonists if they want to keep up the good narrative foundation here and not go down the boring route of rinse/repeat sequels.
As John McClane asked "how can the same thing happen to the same guy twice" - the moral (which of course Die Hard itself ignored - is move the narrative on don't keep trying to repeat it.
I figure they could have one more go at this if it turns out Ted's around but even that would risk being lame.