Huh, really interesting stuff. Definitely not quite what we had theorized it would be like, but certainly even more intriguing in how it's planned to work. I personally hope these elementals are left for special encounters rather than being bound to any one zone. If you can only find a certain element at the beginning of the game or at the end it'd take some of the variety out of the experience of interacting with every element throughout your journey at random. Rather, it'd be kind of drab if the elementals only ever appeared sequentially to fit the zones you progress through. Unless of course zones could be encountered in random order as well?
Going off of the Mana series comparison, an interesting system throughout those games (at least Secret of Mana and Seiken Densetsu 3, the two I actually played for any length of time) was using the different elementals to represent days of the week, essentially integrating the magic system into the passage of time. Maybe not the best implementation ever, as it really ends up just making elemental potencies a situational matter rather than something that can really be manipulated by players or enemies to their advantage. I know I never purposefully slept at an inn multiple times just to sway the elemental preference in my favor, but that's just me.
I wonder what else might shift the potency, occurrence or even the core effects of the elements on the player and on enemies? I could see Elemental Altars as a potential system within the game; I know Elementals have been established as an enemy type, but I'm sure not all elementally-attributed entities aren't inherently bad, so maybe elemental sprites would appear at these altars, and giving them a valuable item or amount of gold would allow you to gain unique benefits from them while possibly also aggravating that element's opposing force, making encounters with rivaling elementals more common.
It wouldn't have to be polar opposites either, just to keep things even more unexpectable. Maybe you can learn element relationships from these sprites, like that Fury elementals have a beef with Sunder elementals because one crashed the other's awesome party, so if you worship Sunder you'll suddenly be assaulted by onslaughts on falling exploding boxes rained down upon you by angry Fury elementals!
Maybe you could also use altars to summon a sprite, then choose to kill it as it's distracted taking whatever offering you set down for it. By doing so, you'd get both your offering back as well as the item or buff you'd normally get fitting that element's concepts, but you'd also invoke the wrath of that element for the rest of your playthrough, making the threat of random attacks from elementals of that type much more common. Imagine doing that multiple times, so that you had 3 or 4 elementals all hot on your tail at once. A scary thought for sure.
Last thing before I'm done, going back to the idea of being granted items by elemental sprites: How about a Berserker Shield received from a Fury altar? It would make any enemy that you shield bash fly backwards with the force of a bomb explosion. Stuff like that could be really fun to play around with.