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I think a could way they could spin it, if making him distinct with Thanos is a MAJOR concern, is to make Darkseid the "internal evil" to Thanos "external evil"
Thanos is the guy who shows up with the disposable space armada and runs roughshod over the place
Darkseid (or more like, his minions) infiltrate a world and gradually make it more unstable and terrible until it becomes another miserable fire-pit laced hellhole where the only supplication the people have is to worship an evil god
Thanos as a warning shouted by cosmic visitors, Darkseid as the word formed by the last breath of a desperate madman who has murdered his family before comitting suicide
Space Conqueror VS Space Devil, in other words.
