It was the first FF game to feature playable characters with any kind of personality, and even though they weren't nearly as deep as those in later games, they were definitely distinctive. The first main character death in the series is still a prime competitor for the most heart-wrenching. Also, FFIV's system of adding or subtracting characters from the active party as the storyline dictated, instead of sticking you with the same ones throughout the entire game or letting you pick freely among them all, was taken from FFII.

It introduced to the series boss music, taunting subvillains, Dragon Knights, Leviathan, Cid, and for goodness's sake, chocobos. It founded the inspiration for môguri much like how Garland founded the inspiration for the Dark Knight concept. And you can't tell me Lionheart isn't a total proto-Cain.