Yeah, it's obvious to me Square was intending it to be a surprise. After all, for the first half of the game, Ghestal was the big-bad giving all the orders, and Kefka was the guy executing them.
People say that FFVI have two main-characters(Terra for the WoB and Celes for the WoR), but I allways thought the same could be said for the villains. Ghestal was the one for the WoB and Kefka was the one for the WoR.

However I don't think the Floating-Continent not being the final-dungeon was supposed to be a big surprise. After all, they did the same in FFII(Mateus' fortress inside the tornado and your fight with him at the end of it), and FFIII(the crystal tower where you fight Zande).