I think it’s because he’s one of the few big cosmic threats that’s a character and not just a plot device. Characters like the Anti-moniter for example don’t have much in the way of a back story or much of personality really. But Darkseid has the whole Fourth world mythos to fall back on. He’s also more then just a big cosmically powered brute. He can play the part of all powerful conquer, but he can also play the part of the schemer. Most other big bads are kind of one note.
Really the only other big bad I feel rivals him as far as having an interesting back story is Trigon.