1) The Flash
Once again Darkseid outranks another hero in The Flash considering he has super speed and teleportation – this is assuming teleportation is better since it’s instant instead of just super fast. Even with a heightened (speed-wise) healing ability, Barry Allen seems to be incredibly vulnerable to Darkseid’s strengths.
But the Scarlet Speedster has unique abilities that will likely come to be useful against the formidable foe. Allen can control the speed force (from which he derives his power) and therefore can control time. While it’s hard to lay a finger on what specifically this will come to mean for the Justice League movie, it’s safe to say time travel often comes into play in larger than life comic book films.
Because Darkseid, too, has (more limited) time travel abilities it could come to the point where only The Flash can stand against him. This scenario happened in the event series Final Crisis, when only The Flash could stop a bullet Darkseid sent through time itself to kill a hero.
(Bonus) Green Lantern
Since the only official bit of Green Lantern in the DCEU is Green Lantern Corps slated for 2020 – the year after Justice League: Part Two – there’s little reason to think we’d see a lantern in Part One. But the intergalactic war that would come from Earth heroes battling Darkseid would at least serve to introduce the Lantern Corps. The Corps’ entire purpose is to be the intergalactic defense of every world using the universe’s ultimate power, Lantern Light. It is possible that Green Lantern will be a key player in resolving the conflict with Darkseid if it (likely) spans the length of the two films.
As of now, “Carrie” Ferris is one of the few characters outside the core team slated for the first Justice League film. Known normally as Carol, Ms. Ferris is the long time love interest of the first Lantern Corps member from Earth, Hal Jordan. Of course Carol is a Lantern in her own right, though a different color on the spectrum. She is the most famous Violet Lantern, whose corps operates separately from that of the Green Lanterns. As of now it’s unknown if Jordan will be the DCEU’s Green Lantern, but it’s clear that the building blocks are already in place to introduce Green Lantern to the universe.
Overall, each hero would be challenged individually by the powers Darkseid holds. But the real reason he would be the best Justice League movie villain is that he would still challenge them all as a team. In fact, it would make sense that Darkseid is the exact reason these heroes chose to team up in the first place. He is essentially the most formidable being in the universe, so who better would the Justice League face in their big screen debut?