it's prolly too late in the game, but I thought of something interesting, where you could do a chapter in the enemies shoes, kind of like the beginning of the game where you are the soldiers, only with any combination including or excluding gestahl, kefka, celes, and leo. They could be accompanies by foot and magicite soldiers.. (the foot soldier is locke's sprite when he steals soldier clothes) It would be interesting to play as the enemy at one point in the game, just for a chapter like at the lete river where mog lets you choose different chapters.
you could have Mog, another moogle, or kappa, or a chocobo for all you care do that thing again where it pauses the game and then lets you choose between doing the enemy subquest and the regular part of the game
The only hard thing would be to decide when to have the event take place, and where, and how to do the events, this could give you more insight into, and strengthen all of the characters stories, but particularly celes or leo. It still would be cool to actually be able to play as Kefka or Gestahl briefly though since it is possible and would enrich the experience.
EDIT -- or as an alternative, you could do another chapter that has Sabin/Matthew doing training with Duncan, either before you meet him or maybe they go off for a short time once you find him in the WoR as a sort of spiritual quest or something. Anyways it would work with Duncan being a pallete swap of Banon and all, and would be a cool isolated quest. You'd have to get rid of Pray though, or maybe you could keep it, but it would be cool if Duncan was different from Banon, and had some cool blitzes or something. It'd just be cool to play as him briefly.
Also I guess you could meet the Returners again but that wouldn't have as much relevance.
We have EVEN MORE themes now, but some old ones are gone...