First of all it is getting kind of tiring hearing everyone call Darkseid a pussy. Why? Because he got cheaply beaten by Superman? When though? The only cheap win I remember is when Superman took darkseid to the sun, then eventually put him in the source wall. However, why is this cheap? Think about it, Darkseid has no super-speed, and on this instance Superman actually decided to use his speed, which he he doesn't do that much normally and against Darkseid I dont' remember him ever speed-blitzing him. So he blitzed him, took him to the sun, shoved his face into the sun, then took him to the source wall. It's not like he kicked him the balls and Darkseid began to cry.
Darkseid has also done some pretty impressive stuff post crisis, like defeating the infinity man.
Now that my rant is over, Darkseid surely can't one shot Superman or Thanos. PC "I put mon-el into a coma with a glancing bitchslap" Darkseid is another story.
Now onto the topic at hand, Thanos does indeed win. Thanos has proven that he is physically superior to people who are capable of destroying planets with their bare hands. So he's got the strength to keep up. Thanos has an insane level of durability going for him, and has survived beatings from both Tyrant and Odin.
Prime is indeed powerful. Strong enough to move planets, much faster than the speed of light, powerful enough to break out of the phantom zone without any technology. However I don't see him winning and here is why: He simply isn't strong enough to hurt Thanos. Yes SBP is strong enough to move planets, but Thanos has taken attacks of a larger magnitude and still been unharmed.
Now, I would say that this would be a stalemate due to Thanos being too durable to hurt and Prime being too fast for Thanos to hit, but if memory serves me right Thanos has some devastating mental attacks that can be released as area attacks which means there is no dodging them.
If I am wrong about that last detail than I will change my opinion from Thanos winning back to a stalemate. But sorry guys, SBP, as powerful as he is, is nowhere near guys like Odin and Tyrant