I'd like;

1) XIIs Gambit System adapted for Companions, because my Chocobo is very very dumb...

2) XIs Trusts system, that lets you summon various NPCs as compansions...

The Trusts style companions could give some love to things like the old Class/Job quest NPCs who've kinda been forgotten. They'd be fairly static in their appearance/skill set, while the current Chocobo Companion would be more customizable. I think that strikes a fairly nice balance...