Just basing off regular FF experience, I can see a few recurring creatures being involved in this. Bombs, oh dear lord, bombs. They will end forts if they explode before being killed. Gel/flan will be rather hard to kill unless affected by the element they're colored after instead of physically attacked (great for adventuring). I think elementals would be rather insane to deal with as well (similar issue with the gel/flan, except opposing elements to kill with). Essentially anything with an elemental modifier would in general be difficult to kill, especially if physical attacks are rendered moot against them. Unless you can enchant armor in fort mode, I think you've got a meat grinder attacking your place.
EDIT:
FF EXP: 986645860 EXP
LVL. 99
But seriously, I am as far experienced as any other kid was playing since the 90s. So my experience is with FF4, 6, 7, X, X-2, and XII, Tactics and Dissidia (got more background on Espers and the heroes/villains of the other games). I had an SNES but no NES back then, and never got around to playing the ones I missed. Just as well, I only managed to afford 7, but not the others (time and money); yet another to remedy. As for next-next-gen with XIII and onward, I dunno; kinda heard that XIII was a bit of a disappointment that was far too linear. Then again, I also don't own a PS3 or XB360 anyway; and if/when I could afford to get either, I think I would just invest in rebuilds of the classics I played anyway for their previous systems (Shadow of the Colossus with a PS3 upgrade? worth it).
If you want to include some of the other games' elements, I would love to see magitek armor in use as mounts, but they might be a bit difficult to program to stay still and not die without pilots.