The problem isn't the story of UX per se, it's the form. Nomura tried to have it both ways: He wanted to make UX a mobile game with a much narrower appeal than other forms of games, but he also wanted its story to be increasingly relevant and necessary. That was the biggest mistake to me. And yes, I do believe it hampered KH3's story to a good extent.
See, the thing is, if the UX story had been released as a console title, or even a handheld title, from the beginning, then it wouldn't be that big of a deal, because A) people actually LIKE those kinds of games, and B) people wouldn't have to hang on through 3 years of filler just to learn important information.
But because only the hardcore fans would even touch a mobile game—let alone a mobile game whose story dragged on for YEARS with VERY LITTLE of importance actually happening leading up to 3's release—it severely impacted the enjoyability of 3's story. KH3 tried too hard to please everyone—it wanted to reward devoted fans who'd spent years playing the mobile game and learning all the backstory and lore, but it also tried to play catchup for the newcomers, which ended up pissing off both camps.
Personally, I think 3 could have done with less than half the references to UX, or even close to none at all. It really didn't need to lean on it so much. And frankly, I think the only reason there WERE so many references was because Nomura wanted to pull eyes to the mobile game to grow its audience: "Oh, you guys don't understand what these people are talking about? Well, lucky for you, there's a FREE mobile game you can download to learn more..."
I think UX has done immense damage to this series in general, if I may be so blunt. The series was hard to follow and expensive to keep up with before, for sure. And DDD didn't help in regards to the convolutedness of the narrative. But by god, I would have taken twenty more DDD's instead of a bland, plodding, free-to-play pay-to-win cashgrab that only justifies its existence by leeching its tendrils into the story of the games people ACTUALLY want to play. Hell, at least DDD was FUN for all its ridiculous plot!
Honestly, I really do believe that KH3 would have been better if UX had just come after it instead of before, as the first installment of the new saga. Pretty much everything in KH3 that has to do with UX's story, you could have cut out. We didn't need the references to Marluxia and Larxene's backstories; we didn't need to see Ephemer at the KG in order to understand that the past Keyblade wielders were saving Sora; we didn't need to see Ven reunite with Chirithy, not that makes any goddamn sense anyway; we didn't need to hear "may your heart be your guiding key" ten thousand times; Maleficent looking for the box could have alluded to her time traveling in the UX story without us having to know about it beforehand (Example: Pete: "Hey, uh, Maleficent, where'd ya hear about this box, again?" Maleficent: "An old friend told me. Maybe someday I shall tell you as well...").
Actually, come to think of it, the whole box thing would have worked better if they HADN'T released Back Cover first! Think about it: If not for BC, then we wouldn't have had any expectations of seeing what was in it, because it wouldn't have been built up. On the other hand, if they'd introduced the box in 3 and then did Back Cover AFTER, then it gives us backstory to the box in a way that expands our knowledge of it without actually revealing what's inside it. The way they did it, it just ended up feeling like a bait-and-switch.
Everything else having to do with Daybreak Town could have been kept in, and they would work better, because it would have built up what Daybreak Town was, the same way CoM built up Twilight Town before actually revealing it in KH2.
Really, the only thing you'd need to have played UX to understand is the Xigbar/Luxu reveal and the return of the Foretellers at the end of the game. Other than that, I can't think of a good reason why all the UX stuff couldn't have just been put off until after KH3 was released, and cut out most of the references. It would have made the story feel much less crowded, much less confusing, and much less artificial. But as it is, UX remains a permanent scar on KH3's plot. And I pray to God that Nomura doesn't make the same mistake with another title in the future.