I see your point.
Neither stories from the games puts them as a menacing face for the protagonists, but my point is they at least appear all the time and are exposed to us players a lot, which is the build up for the end. Between worlds on their giant chairs talking dark gibberish so the player can at least feel something is coming, with random appearances of Org XIII's in disney worlds...
Xehanort also didn't really was active in BBS until the last battle, but I remember playing through the game with the 3 characters and really understanding that the center and focus of the story is around Xehanort's evil shenanigans, you can feel he is powerful and that he is planning something, so when you get to the end you can actually feel the pay-off that the story was going for throughough TAV's journeys.
That's really different from KH3's xehanort, where we only see him in the end of the game and when it is supposed to be a pay off from a build up, it feels more like starting a build up in the end - which is bad, and that's why the supposed pay off didn't really hit hard as it could for many people...
I also felt the same with DDD - but I think they managed to make it better than KH3 in that sense - because Sora's last world in TWTNW can feel like a build up for something that is about to happen in the end - that being Riku saving Sora's ass from being norted. However the villain's random appearances through Disney worlds are really cheap and deliver basically anything .-. but at least there was SOME build up to the end, so it feels a little satisfying to get there.
I actually felt more satisfied in KH3 going to fight Xehanort than I did Xemnas in KH2. The sole reason why is that Xehanort in KH3 had the advantage of basically every game in the series leading up to this fight - in one way or another. This isn't commentary on KH3's plot/pacing because that was problematic. Rather, Xehanort in KH3 had it easier to be seen as the final villain since, well, he was the final villain that we've been waiting to beat with Sora since we discovered all the background stuff he's been doing. Xemnas suffered because he was an absolute mystery (barely referenced - not even by name - in CoM) and his game basically had him appear a handful of times at the start of the game, then vanish for a few hours with only brief/meaningless Organization member encounters, then reappear for the middle of the game for an epic moment, then vanish again for hours, then reappear for the end of the game (Twilight Town into TWTNW).
You're right about BbS Xehanort which I think worked for a side game. Xehanort wasn't established as THE main villain yet and at the time of BbS' release, we assumed that all the Norts were dead (and couldn't come back). Back in the BbS days (lol), I actually took BbS as Xehanort's backstory game, as well as fleshing out the keyblade's lore.
To circle back to this thread... it would be painfully repetitive to have another villain just pop in at the start of the game, vanish, have cutscenes babbling vague nonsense far away, then pop in again a few hours later, rinse and repeat until the final boss fight. I say Nomura, switch it up. DISNEY doesn't want to give you boss fights in worlds, then throw some Foretellers in there. I think that would be a creative way to re-use older worlds that many fans claim are "done to death". It would also help maintain MoM's presence in an active way throughout. I mean, like you said about them talking gibberish on giant chairs... I let Nomura get away with that with the Organization because seemingly everyone had their own agenda and/or it was to their benefit to not give all details to each other. But if you really think about it, why would partners in a group talk to each other so vaguely? The sole reason why is because it's a cutscene for the players to watch, but Nomura doesn't want to give away anything. I'm really hoping for a change in how the villain(s) are handled in future KH games.
The mystery worked for Xehanort and right now it works for the MoM, especially because we were hyped to KH3... but now that KH3 and ReMIND are done, it's time for the MoM to stop being so mysterious. I know part of the reason Xehanort was so mysterious was (realistically) that Nomura was making it up as he went on/didn't know where he wanted to go with the story, but had ideas that he wanted to introduce. I'm hoping that Nomura knows where he wants to go, that way the MoM can be handled properly and thus not need his own game or movie.