Thanos and Darkseid are two sides of the same coin. Though they don't share the same creators (Thanos was created by Jim Starlin and Darkseid by Jack Kirby), they do share similar origins and roles in their respective universes. Both are part of, in some way, all-powerful cosmic races created by Jack Kirby -- DC's New Gods and Marvel's Eternals (co-created with Martin A. Burnstein). As all-powerful forces who have been the source of universal, and even multiversal devastation, the Mad Titan and the Lord of Apokolips are often held in equal standing. However, there is one respect where Marvel's cosmic titan is better than DC's.
Both have shown themselves capable of universal destruction, there is no doubt about that. Thanks to the Marvel Cinematic Universe, everyone knows about Thanos successfully wiping out half of all life in the universe. Although the Avengers undid this both on-screen and in the comics, it happened and its effects are still felt to this day. Darkseid on the other hand has laid waste to multiple universes with the Anti-Life Equation and almost succeeded on more than one occasion in the main DC Universe. Though he hasn't crushed DC's heroes yet, he's come very close.
So why is Thanos better than Darkseid? The infamous New God came closer to achieving his goals more often than the Mad Titan. The very thing that makes Marvel's character a better villain than DC's is also the exact thing that makes him a weaker one -- his humanity... for lack of a better word.
Thanos hasn't always been a straight villain. He's actually even sided with the heroes a number of times throughout the years. He teamed up with the villain Annihilus and played a big part in his twisted plans for the universe, but when he found out that the villain actually planned to destroy the universe, he betrayed him. He helped Marvel's heroes save reality from all-out destruction, which is pretty heroic.
There have been many other instances too. He may not have been a good father to her, but he did save Gamora. He also aided the Silver Surfer in stopping a rampaging Thor from destroying Asgard. He even saved the Marvel Universe from the Cancerverse by helping the Guardians bring Death to it. He was also a "hero," again for lack of a better word, during the Infinity War and Infinity Crusade events, and even switched sides to stop an Infinity Gauntlet-powered Nebula at the end of the Infinity Gauntlet story. It's undeniable then that there's a part of Thanos that isn't at least a little bit good... or at least ambitious, which can sometimes rub shoulders with good.
Darkseid, on the other hand, is all evil. The only good deed he's ever done is taking on a resurrected Doomsday, and that was only to protect his own planet of Apokolips. If given the opportunity, he would weaponize Superman's killer in a heartbeat and unleash him upon Earth. He's even tried to do that with Superman and Supergirl before. In Final Crisis, he was able to corrupt Wonder Woman and have her lead his Anti-Life army. That's barely scratching the surface of everything he's done.
The fact is, Darkseid is a multiversal constant. There may be other versions of him in other universes, and some of them may turn out to be good, but they aren't the real deal. Thanos is different. He isn't the embodiment of all the multiverse's darkness and evil like Darkseid is. Nor is he a god like Darkseid is.
Thanos is far closer to human than many would like to admit, and it's that sort of frailty that often undermines his ultimate victory -- a fact he's noted about himself. The rare glimpses of compassion he's shown for others make him a far more interesting and complex character than his DC counterpart, and thus, make him a more compelling villain. The capacity for good, and his grappling / ultimate denial of it, gives a villain more pathos. There may not be an all evil version of the Mad Titan out there, but that's a good thing. Darkseid can be a catalyst for creating interesting and compelling characters in DC's stories, but Thanos already is one.