Linkshell Airships
Skillchains and Magic Bursts or something similar
Generally, more interesting and tactical basic combat
World bosses, like the dragons in XI, but with less crazy spawning conditions so they aren't camp/bot-fests.
Non-instanced dungeons
A golden-saucer type place. Always thought that would be a fun idea for an MMO. And it could act as a gil-sink instead of crazy fees on other stuff.
Materia that gives more than just stat boosts. Maybe specific skills, or cosmetic enhancements, or run speed increases, etc.