This could be as simple as just auto getting it when you hit certain benchmarks. 1 favor every 2 slayer levels +1 when you finish. 1 every 2 or 3 explorer +1 when you find them all. 1 for each rare encounter. Who the favor is for would depend of the wilderness encounter, Coin Lords for Waterworks, Free Agents for Cerulean Hills, etc.
What would be better however is if you added story to those.
Slayer example: The first guard in the water works gives you the 10 and then 25 slayer quests. He gives you 1 favor after 25. Then the second guard gives you the next 2. You could then add other NPC in different spots near the enterance, maybe from different factions even, each having a new reason for you to kill stuff.
Explorer: scatter some NPC's outside the wilderness area (much like the collectors) that want certain locations found, for some reason. Once you find there list of places, you go back and they give you favor.
Rare Encounters: You find it, kill it, in the loot chest (if it isn't a repeat occurance) is an item that is connected to an NPC. Bring it to him.....bam favor.
I think this would go along way removing the only thing that has felt like grind (to me anyway) in the game. Not to mention that anytime you add story is a good thing.