I think the best way to implement jobs is the way they're doing it, however...
I feel that these jobs quests should put you in situations that you work with NPCs and have to learn your class to finish each mission, a different skill with each mission, with the final mission being a cumulative effort. Like each quest is homework and the final quest is a test to see if you're worthy of using that job in endgame. And I mean the final quest should be HARD and something that only the best of the best of each job can do, ones that try their hardest and are prepared.

Like PLDs will have to keep hate off NPCs and tank, WHM's will have to heal multiple people, one target, WAR will have to do enough damage utilizing their skills in enough time, etcetc. I don't think you it should tell you EXACTLY how to play your class, as to leave room for theorycraft and otherwise, but I think it should cover the basics in the end.