I'm more partial towards the idea of a auto-jump, like in FFXIII, for multiple reasons. Overall, it would be easier to implement. Less changes would need to be made to the game itself. Less testing for exploits, and really, fewer chances of getting bugs, since it would only be used in situations the developers plan for, not everywhere they dont.

That said, im not really against the idea of a free jump. I would enjoy a free jump if it was used in ways to make the game more interesting, such as through more complex fights, but really I dont feel it's necessary. Plenty of games, console and mmo alike, dont have a jump feature. It's just not necessary for some games.