I think the major problem currently with the Hunts is that they are the only decent source of Allied Seals currently. My suggestion would be have a certain Fates give Allied Seals for successfully completing them. The Fates I think should have Allied Seal rewards are:

Lazy for You
Attack of Highbridge: Act III
It's Not Lupus
Clearing the Hive
Defending the Hive
Keeping the Hive
The Eyes Have It
Dark Devices - The End
Go, Go, Gorgimeria
He taketh It wiith His Eyes
Steel Reign