I'd quite like them to revamp the entire Companion system, so it isn't just Chocobros, but also various NPCs, then add new quests for Class/Jobs which allow you to unlock various NPCs for that system. That would be what? Twenty two Classes/Jobs? Some with potential for multiple NPCs and thus multiple quests? Would be a nice way to give us some more Class/Job lore and give us something meaningful as far as gameplay goes... Imagine having Rielle as a healer Companion, of Sid as a tank. Chocobro can still be relevant seeing as we can customize it, but having NPCs would be a nice option for people who don't have the time (and money) to level their Chocobro to the cap. Throw in the Gambit system I'm fairly sure was mentioned for Chocobros during beta while we're at it...
Only issue I can perhaps see is multiple people having Rielle out at the same time (or even having Rielle as a pet, you monsters), but I don't personally find that too immersion breaking... Would love to have a post-cap catch up with the various Class/Job NPCs, though I suppose that might clash with future cap rises... Heck, you could arguably even throw in crafting and gathering Classes to the mix... Thinking mostly of the 60 Blacksmith and Armorer quests, but the party from the later works, and you're damn right I want Laurisse instead of a Chocobro! Even the Miner quest had a group that could work as potential Companions...
It would also add potential for "Jobs" which aren't likely to be added... Fairly sure we're not getting Thief, but Jacke could effectively fill that role (Companion with Treasure Hunter!). Likewise, someone wants Puppetmaster? Level Monk and Goldsmith, and get Gigi as a Companion. Lots of possibilities with something like this, both for storylines and open-world gameplay, would add quite a lot of depth I think.
That's how I wished they'd handled Esoterics gear... Have a repeatable Job quest to obtain antiquated gear, with some nice lore and mini-trials involved... Could still tie it to tomestones and apply the weekly cap, by having the quest go "Bring my X Rowena's Tokens (Esoterics)", but it would have been far more interesting than just tomestones... I'm honestly bored of tomestones at this point... AF2 with no Job related quests was a big missed opportunity IMO. Could have spiced up the grind and given us some nice Job lore at the same time...