I think there are ways they can differentiate Darkseid from Thanos. Granted most of my knowledge about Thanos' mythos comes from reading a summary on Marvel wiki and outside of getting the Infinity Gauntlet I'm not sure how Thanos' plot will end up in the MCU, but I think there are some differences they can play up. Their appearances are somewhat similar but there are differences that set them apart. One has purple skin with gold armor, the other has grey skin, red eyes and wears black. They can give Darkseid a more stone-like skin texture, structure his face in a way that resembles the comics but looks less like Thanos. They have a similar look and build but there are differences.
But the biggest difference, assuming they use Darkseid's anti-life equation as his end game, Darkseid is basically the Devil that wants to control all living things to be slaves at his mercy. Where as Thanos' wants to use the Infinity Gauntlet to destroy all living things to impress "Death". Darkseid wants total dominion over all living things to be the Universes ultimate tyrant dictator, turning all livings things into mindless slaves. For me personally if done well, I find Darkseid's plan to be more intriguing and less generic than just wanting to destroy everything, and he's not doing it to impress anyone, it's his own plan for domination. Darkseid is more of Satan analogy and should be a darker character, with his plan leading to a comic book version of the "Mark of the Beast", depending on if they go that route. I'm not sure what Thanos' end game is supposed to be, to destroy everything and live with "Death" as the only beings left?
Darkseid has a different set of allies, with DeSaad, Goodness, Godfrey, Parademons and the Female Furies and rules his own Hell-like Planet (Which I'm hoping we will see alot of once he's introduced in the DCU). I'm not sure what Marvel with do with Titan, a moon of Saturn and his army, I don't know as much about his allies. I've read they are another robot army, which is becoming a tired trope. There are some similarities there, though I don't know how much they are going to play up either characters base of operations.
Both have God level backgrounds, but so do other characters (Wonder Woman, Thor, Ares, etc.), it's impossible to avoid, they'll just have to play up any differences in those mythologies as much as possible.
Anyway, point being there are some pretty big differences they can use to differentiate the characters, though there will always be comparisons as there are also some parallels between the characters. Maybe someone more well versed in each characters themes can explain it better than me. Admittedly I'm working with a limited knowledge of both characters, particularly Thanos.
