There is really only two things I think they should do with Hunts;

Stop putting gear upgrades behind them. Hunts are not remotely challenging. They are not remotely interesting. They're a pure zergfest, get an invite and faceroll your keyboard. When they didn't offer gear upgrades, and thus were fairly unpopular, then I think Hunts worked as intended. They still weren't particularly good challenges, but at least they weren't completely pathetic thanks to the entire server jumping on them. So yeah, remove the gear upgrades and let the content be some side thing for glamours or something, they worked like that.

Alternatively though, I'd much rather see Hunts remain as endgame content, I'd just much rather see them boosted to a level that isn't pathetic. Force pops, same as Treasure Maps, but better. Only your party can touch them. Only your party gets touched by them. Done, now you can make the encounters interesting and challenging. Leave B Ranks and the Mark Bills as is, let people do those to earn some starter Seals, with those they buy pop items to challenge A/S Ranks. Have A/S Ranks drop trophies, which in turn can be used to buy pop items for even tougher Hunts. Basically, just go look at FFXIs ZNMs, that is an open world NM system done right. Only addition I'd perhaps like to see is actual hunting involved, rather than static pop items and locations... Perhaps have a Hunt NPC in each zone who will keep you updated on the targets in that zone and provide a sort of mini-quest to spawn them; He tells you what the target was hunting, that tells you your pop item. He also tells you were it was last seen, that points you in the direction of the spawn location. Perhaps when you get to the spawn location you only find tracks leading off somewhere else. Perhaps the NPC can also tell you the Hunt target was butting heads with another Hunt target, and when you get to the location you find two sets of tracks, one leading to your intended target, the other leading to the target it was fighting. Perhaps have a dud in place, so if you're a "bad" Hunter, you can end up wasting your pop item on something completely irrelevant because you didn't follow the tracks closely enough (I'm imaging having different sets of tracks to follow, and if you're unaware of what type of enemy your target is, you could end up following the wrong set).

I would eat content like that up. It is mechanically interesting, rather than "herp derp>> /shout X is up @ <pos>". As far as fights go they are as challenging as you want them to be, though they can out right be made more challenging anyway. Want to try and solo it? Go for it. It's your pop, not something the entire server seems entitled to. The only interesting thing current Hunts offer is perhaps the S Rank spawn conditions, but they seem pretty disconnected even as conditions (you can be meeting the conditions, have it spawn, and be completely unaware). Could still have a system like that in place with force pops anyway, although some of them wouldn't work (like FATEs), but you could easily have requirements like "Must have a minion out", or "Must have La Noscean Leeks in inventory", though perhaps instead change them to optional things which "weaken" the Hunt, plenty of quests have us going after an enemy and giving us an item that will weaken it, perhaps make S Ranks similar to that; "If you have a minion out, it doesn't get a damage buff". Heck, the conditions could just be exactly as they are, but rather than spawning the S Rank, they open a window in which the Hunt NPC will tell you where to go looking. Server works together to meet the condition, Hunt NPC sends groups off in different locations looking for their pop location, few hours later the window closes.

Honestly, there is just far more you can do with force pops, than you can with world pops. You have a might tighter frame to balance them in. You can remove almost all drama. You can try different and more complex mechanics, both in the fights and in the spawning of. Overall it would just make for a better quality of content, rather than the glorified FATE bosses we currently have.