I thought of another good one last night;
More character interaction between co-stars. Final Fantasy X did a phenomenal job with this. Characters had their own backstories, and many of them were related, and they would speak to each other in a different tone or an a different level than they would speak to the main character. Especially when Rikku came into the mix, and Wakka's whole not-liking-those-kind-of-people thing. It really humanized the whole experience.
FF6, 7, 8, and 9 were also pretty good with this. 6 especially since there was more than one "main character." FF12 kind of dropped it, though.
Other recent games haven't done this too well. Take Mass Effect, for example. Sure, the interaction between the main character and everyone else was stellar, and a huge step up because you had so many dialog options and choices about what you could do and say, but there wasn't even an inkling of interaction between ANY of your teammates. The Quarian chick never even spoke to Wrex, Ashley didn't give a shit about the Taurian guy, etc... I mean, all these people are together on a ship for a long-ass time, and saving the galaxy together, you'd think they'd try to get to know each other, not just the main character.
I'm just tired of games that represent the old style of RPG's, like Final Fantasy II. You knew the characters in FF2 were childhood friends .... because the dialog box TOLD you at the beginning of the game. They pretty much never speak to each other in the entire game...