First, being able to avoid earth based attacks by way of jumps would be broken. Especially since you get the warning, it wouldn't be hard to time, which stops anyone from ever going an earth route, especially in PvP, but also, the earth attacks rise a bit from the ground, so even then, I doubt jumping is gonna stop them unless you're using a Dragoon Jump.

Also, you could still do stuff like the floating platforms, even in an automatic setting. The problem is though, to avoid terrain abuse, the ability to target to many levels above or below you is off, and even if you do, monsters can move up most any terrain. Same deal with swimming. There's gonna be a lot involved with going in the water. Now, I think an underwater temple is cool as hell, and I'm just as for it as the next person, but I just do not wanna deal with under water fighting. Of course, then again, I think they have something planned with airship battles, so trying to rule out to much is silly too, but if that stuff is gonna show up, it's better off in the form of some addition to the regular movement mechanic. In other words, no up and down movements. Set paths, even under water. What's more, a lot of the water in the game isn't even set for something like swimming. The Ocean in Limsa is a solid object. It's basically a specially textured ground. Since they're not about to change any of the current maps as is, I doubt they're gonna over haul the water of La Noscea any time soon. More importantly, there's a LOT of other stuff I'd rather see changed and overhauled than trying to do swimming. Swimming alone would take probably 3-4 months just to develop, and another 2 to implement and get actually working. That's 6 months I'd rather see spent on more meaningful things.

The best way to handle jumping is just a smooth add-on to the basic movement mechanic. As far as I see anyway. Its a quick trip to the MoCap studio, about a week to get it all mapped, and bam. You're gold.