I saw somebody else in here mention that they hope it gets converted to a single player offline game sometime. I have no idea how they'd do that and I think the odds are a million to one, but if they ever did that I'd buy it right up. Though I haven't played in years, it'll be a sad day when the servers go offline.
Now that the Trust system gives several NPCs combat data, it would be a matter of having them join your party after the relevant cutscenes where they appear (or leave if the cutscenes lean that way too) - for example, Lion could join early in the nation missions, leave at the end of Zilart, and possibly return after Apocalypse Nigh.
Enable full alliances with NPCs - That should make fights like Provenance Warden viable.
Integrate the adventuring fellow system with the Trust one.
The auction house would be the major issue - it'd have to be resupplied in some automatic periodic manner.
If you changed nations after some mission progress, the common Jeuno-related missions wouldn't have to be repeated, and if applicable, Kam'lanaut would be replaced by Esch'ntarl.
Making the whole game a single unit not divided by expansions could also help address some issues in the game's current state, like the binding job-specific quests to areas related to the job's corresponding expansion, or the fact that in a mythology-heavy story like Chains of Promathia we don't get to visit the Hall of the Gods because it's a Rise of the Zilart area.
Adjust the drop rates on everything, as well as the amount of items required to upgrade anything.
Reward quest completion with EXP everywhere, since that was only implemented by Seekers of Adoulin.
Unify the teleport systems current in place through features like the home point systems and Survival Guide books.
Don't make glowing spawn point like those for Voidwatch appear until that quest line's been initiated, it breaks immersion in areas if it's not relevant yet.
As for NPC AI to enable mechanics, I hear XII took steps in such a direction...