the northern crater in disk three could be a good place, multiple places in there that would be nice to place a super boss in, but with lack of save spots, that can be a bad thing (or use up the save crystal near the super boss, to make things easier). the back of the forest opened by killing ultimate weapon (where you find the (i think... been a while) apocalypse for cloud), placing it in the end area there could be nice, but requiring you to trek back through the forest.
it also depends on what your ultimate enemy will be... if it is humanoid, you could have it easily fit into towns and such (create an npc that is actually the enemy), then you could do things like place it in the back of wall market, or in the center of kalm, since there is already a quest dealing with kalm. if it were to be something big (like a recreated omega weapon or something) it would need plenty of room, and unless it were to attack a city, then it wouldn't really fit in too well.
a mako created enemy could fit into mt. nibel, possibly in the reactor itself if you can reenter it later in the game, or just somewhere in the surrounding caverns. if you could make it so that the area where aerith was killed was accessible after doing something (possibly a side quest, or just making it able to be accessed at any time after that event (early game ultimate boss possible O_o)), then that little place could be a great spot for the fight, an ancient monster coming out to play. there are many possibilities, but i need to know the type of monster first, and what you are capable of doing
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making the materia accessible earlier can be good and bad, especially since the places are all available at the end of the first disk since chocobo breeding is open then (i think it starts end of disk one, before the second... i have to check on that).having the end game materia possible early on isn't entirely a good thing. i don't know what all is doable with the battle square, but would you be able to add the materia as rewards from there, which are only available on disk two/three (whenever you think it is the best time to have them), and are only able to be gotten one time (like omnislash). this could also be done with the gp (i think?) from the game corner (or whatever it is called with the minigames >_>), but since the guy at the entrance sells gp, it could be done pretty easily if you have the funds, though it could still be worth it if the battle square isn't as easily done.
it would be really nice if enemies could drop materia, but since that isn't done as easily (can be if you edit the field files for enemies that appear on the field, like boss battles and such, or create monster-in-a-box fights which give the materia when opened/enemy defeated, but making the enemy unable to be fled from), it is probably better to do it another way.