I voted KH2 Xemnas.
For starters, it's silly, but I like to have my final bosses with some sort of scale. So that instantly eliminates Reverse Rebirth, Days (unless you look at Xion, but frankly that fight was just ok), coded, and BbS.
With regard to BbS, while it certainly offered some surprise, after the shock wears off, it's really not that great. The first phase is an almost exact copy of Terra's final boss (and I really just didn't enjoy that fight to begin with), and the second phase, while entertaining, is really just a mix of Terra's final boss and KH1 Ansem. So there's hardly any originality. The most enjoyable part is the music.
Reverse/Rebirth, obviously, is just a copy of one fight from the final boss of the first game, so I don't know why you would pick that over KH1.
The fight with Riku in Days is incredibly boring and incredibly easy. The music is nice but... it's just rehashed.
Roxas in coded is more or less a watered down version of Roxas from KH2FM and just uses the same animation from Days.
So then we have KH1, Re:CoM (Sora), and KH2.
Marluxia's out. His first fight is boring (CPU should have been better), second fight is pretty good but I'm not a fan of the music, and the third is awesome (with the best boss music in the series), but not enough to make up for the other two.
Just for the hell of it, I'll break down the KH1/KH2 fights by their individual components, since they have similarities (though not chronologically), and pick a winner in each category.
1. Ansem SoD phase 1 vs Xemnas phase 1: The music in both is great and neither fight is particularly hard, but Xemnas' fight is easy to the point where it's stupid (even though Memory Skyscraper looks cool), so this one goes to KH1.
2. Darkside vs Dragon (ship fight): Darkside, despite looking great, is an incredibly boring fight. The Dragon, while it isn't challenging, offers a bit more variety in gameplay, so this one goes to KH2. A shame we didn't get to fight Twilight Thorn again instead.
3. KH1 "appendages" vs KH2 "appendages": You know. All that other stuff you have to fight outside of actual boss fights. For KH1, it's that mast head on the world of chaos, the jelly "stomach" in it, and saving Donald and Goofy. For KH2, it's dodging the buildings, taking out the jet engines and destroying the reactor core. Neither are particularly challenging, but this one goes to KH1 purely because of the aesthetic- it just looks cooler. The organic look beats out the mechanical one.
4. World of Chaos Phase 1 vs Armor Xemnas Phase 1: This is tough. Fantastic music in both, though Guardando del buio edges out over A Fight to the Death a bit I would say. At the same time, though, the flying mechanic in KH1 was never really good, but it was cool seeing all of the Organization weapons return in the final fight for KH2. Neither is particularly challenging. I'm calling a tie on this one.
5. World of Chaos Phase 2 vs Armor Xemnas Phase 2: The other tough one. The segment of Darkness of the Unknown that plays in KH2 here is my favorite. And while Guardando del buio is great, the fact that it's been playing for some time, it kind of loses some oomph, so KH2 just manages to beat it music wise. Armor Xemnas isn't really as hard as World of Chaos either, but at the same time, his fight is way more fun (with all of the abilities maxed out) and it's much more different than the previous phase of Armor Xemnas, while World of Chaos remains a bit too similar. Plus, just the perspective in the Xemnas fight is great- seeing the whole world being sucked into a giant vortex, buidlings flying everywhere. I'm giving this one to KH2.
6. Ansem SoD Phase 2 vs Xemnas Phase 2: This was the only part of the Xemnas fight which was genuinely challenging (at least on the first tries), while Ansem SoD's fight was pretty formulaic and his attacks were easy to dodge. So difficulty goes to KH2. Music wise, it goes to KH1. While Forze del Male already played for the Riku fight, it's great hearing it here. On the other hand, I was never much of a fan of Darkness of the Unknown part III. Xemnas' environment and range of attacks is also better, so I would give this one to KH2 as well.
Obviously, people won't agree, but as a whole I just found KH2's final fights more entertaining. Not as difficult, but neither game has challenging final boss fights, so it didn't really matter to me. What really hurts KH1 is the damn flying mechanic.