From a lore and gameplay perspective I really enjoyed the thaumaturge class quest and the black mage one. Its awesome.
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The Pugilitst and especially Monk-quests are my absolute favorites.
The Pugilist-quests about the guild being in danger and you having to train with the members is very nicely done.
The Monk-quests about opening your chakra at warzones is also very good and the last fight is challenging as hell, but so much fun!
At the moment, I'm playing Lancer/Dragon and just hit Dragon, with a pretty interesting quest. The Lancer-quests were also quite good, however not comparable to the pugilist's.
Do you know what you did in the level 5 quest? You hit boulders.
Do you know what you did in the level 10 quest? You hit boulders.
By the time you get to level 15, when you're first supposed to start doing dungeons, what are you still doing? Hitting boulders.
And you're okay with this?
Absolutely nothing about tanking in these quests. At least the GLA one teaches you to use Flash to keep hate off the NPC healing you. The CNJ teaches you to juggle targets, while you keep healing NPCs. The ARC ones teach you how to manage adds. THM teaches you to sleep targets. ACN teaches you to use different Carby abilities in different situations.
Next time you wonder why that MRD tank is struggling in early dungeons or maybe doesn't understand what they're supposed to be doing, blame the MRD storyline that taught him nothing about what he was supposed to be doing.