I think at least part of the reason is that he keeps trying to shove it into the Fate framework along with cosmic horror, HFY, and incredible power differentials. It's pretty much a kitchen sink setting at this point which is not readily conducive to good worldbuilding; the only one I can think of that's actually pretty good is Discworld, but Discworld goes for the absurdist approach to worldbuilding anyway.
The other really obvious one, Golarion, is a fucking shitshow and only works because it's not a story but a selection of incompatible settings that barely interact with each other and have stories pretty much confined to one particular region. Nasu, though, can't keep his HFY apart from his cosmic horror and can't keep his weird 'progress is good but not if it's too much progress' philosophy away from the concept of heroic figures who are defined by making more progress in their lives than dozens of lesser men could together. He mixes the concept of heroic journeys with this idea that a hero should somehow be involved with all of humanity, and when he really can't do that he whitewashes, genderbends, pseudoservants, or does some garbage like making Attila an ayy.
So basically I don't know if he's bad at scifi per-se, but Fate is not a setting that's conducive to it. It's not even conducive to itself at this point, without tron line Ishtar.