How Gothel kicked the bucket in the original movie gives some potential for this as a Final boss fight. A fight with Gothel...that segues into a fight with her heartless. (which would be compatible with Zip's concept with the possible exception of the last bit)
The idea is as she falls off the tower, her darkness transform her into a Dust-themed heartless at the last second (my tenative idea is a dust tower theme, as in she assimilates the tower into the Heartless form). Resulting in a 2-stage boss fight a la the Dark Thorn in Beast's Castle or more closely, the Jafar and especially Oogie Boogie boss fights in KH1.
The Heartless boss would be fought in the area outside the tower and would use light, flower and dark attacks. Some of which would be reminiscent of the large spikes that appeared in the cartoon spinoff (speaking of which I hope "Wind in my Hair" is involved in the game somehow). Where Sora and Rapunzel have to scale the tower to defeat several cores, dogging them along the way is a different Heartless boss more loosely inspired by Gothel (and part of the Tower heartless, like the Groundshaker) and some Plant Heartless from past games. That Heartless would be invulnerable but would attack the group with elemental attacks. The Tower's other defenses would be a sandstorm like attack, causing obstacles to fall down from the roof (where the last core resides) and flipping parts of the fllor to throw off our heroes. The tower would also have in addition to scaleable walls, rails that resemble a dark violet version of Rapunzel's hair. Victory int he fight would reuslt in the tower returning to normal and the witch like Heartless mimicking Gothel's demise (falling down, again. and disintegrating into dust)
Course the idea is admittedly derivative, but there is potential for a villain+heartless two stage fight because of the source material.
On a side note, for any Marluxia boss fights, bring back Graceful Assassin! then have unique themes for th rest of the Organization