So, um... idea to split between the two options.

Remember how the Summoner gained a new Job skill and it's older class skill changed it's design and effect slightly, and how the earlier Class quests always had you kill some open world monster before you got to the meat of the quest? Mix these two things.

You go to your Job master, and they tell you to go fight X monsters, then they'll send you off to fight the one that you'll learn the new Job ability from. Once you're done, you'll learn the new job skill, and skills XYZ change to monster based variants of those skills. At fifteen class skills not learned from quests ((Based off Gladiator, numbers may be different for other classes)) and five Job quests from levels 30 to 50, shifting three skills each would cover them all, minus the 15 and 30 abilities.