Right now, everyone is giving all these ideas to fix the hunts by directly changing the system. Many argue that the problem is too many players, either way, yeah, it does suck. Looking outside the system, there is a way to improve many game aspects on top of fixing the hunts.
Make various FATEs give Allied Seals based on medal earned. 90% of the time you will make gold rank, so it's not much of a condition to get the full Seals from a FATE. Having many of the more common ones drop 1 to 3 Seals, but give a LOT more for the commonly ignored NOTORIOUS MONSTER FATES, which have no reason to be beaten more than once. I have not seen anyone beat The Eyes Have It in quite some time. This would make more of the epic FATEs have a reason for players to take on.
An alternative to hunting big targets, a player can grind with a FATE party. Now, those doing FATEs can get some exp as FATEs are constantly getting done. While only certain FATEs will give Seals, players will sweep an area to get Seal type FATEs to spawn.
The need for Seals is great, and will last a LONG time for most players, especially those multi classing.
Ignored FATEs, due to difficulty and lack of reward, now have a purpose once more! They need a LARGE number of players and take a long time to kill, better than Hunting targets being secretly hunted by others. A solid reward for Notorious Monsters!
Hunts will do better with parties, as party participation increases reward chances. This beats doing minimal damage to a hunt and getting no Seals. Now a group gets together and gets rewards together (builds community instead of crushing it!)
Now, I might be biased with this idea, but I can see no problem with it. It'd reinvigorate the FATE system and allow many players a more fair way to get Allied Seals. Of course, hunts would be a nice solid big chunk of Seals to get as your party races between FATEs, but you're no longer running around in a panic trying to be first to find and kill it. It pops, it dies, but more people care less about it instead. It's not the entire way to earn Seals lost, it's just a few, and so the animosity is reduced.
Hunt difficulty should still be significantly increase, even for B ranks, but this is something that could benefit more than just the Hunt.