The Xehanorts definitely have similar goals and motivations (which makes sense) but I've always thought of them as representative of very different means to an ultimate end. Even their mannerisms are starkly contrasted: Ansem SoD is poetically cryptic and uses ornate, sweeping gestures to push his agenda whereas Xemnas is viciously analytical, as well as more subtle and refined in his provocations. Master Xehanort picks up on aspects from each of them and is framed as delectably evil camp rooted in a kind of primal menace. The approaches they use to summon Kingdom Hearts are indicative of this, as well: Ansem sinks whole worlds into darkness while Xemnas concentrates on exploiting the elemental make-up of people (their hearts, memories, associated bits and pieces) which can be contained, studied and deconstructed. Master Xehanort is less roundabout than either of them, and that makes him feel more dangerous: he'll destroy anyone and anything not only as a matter of course, but by way of actively inviting them into his plans. Casualties of friendship and existence become the means to his end-- which appropriately informs Sora's rebuke of the Xehanorts in DDD. YX, by contrast, is way too nebulous for me: I feel like he never makes a mark on the plot which couldn't be substituted with any other bad guy. So it's interesting to hear that others regard him as a favorite.
Larxene and Vexen are great villains, and Saix is almost too good to be given a secondary role. Again, I'd say all of the CoM baddies are superbly realized, with even Lexaeus managing to establish himself in his brief appearance as a force to be reckoned with.
At last, vindication.
Your post reminded me that I liked some of the things you liked, too, like the field and battle music in those worlds. That's generally a given with KH but Shimomura went so free-spirit on DDD that the parts that work really stand out to me.
The Young Xehanort boss fight baffles me, because I don't recall having any issue with it (I don't recall much about it tbh) but people talk of it like there was something uniquely frustrating to it. Meanwhile I always die to the Parasite Cage in KH1, it's downright laughable.
