If you hate that, you're going to hate the Moogles muchly.
To be honest I like the quests that have their own little storyline (the Chocobo Hunters with the Newbie Miqo'te Chocobo hunter keeps going up to level 58)
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(presented out of context to avoid spoilers)
... but I hate the back-and-forth to the same spots over and over. It's less annoying once you get the Chocobo to fly. But keep in mind that that specific zone has no less than three sets of quest givers, so you'll spend a lot of time there and in the next area just doing all the side quests for experience.
As for how SE could improve stuff to be more challenging...
More of those "instanced" storyline type of combat would be fine in the optional quests. As far as I can tell, I don't think there are any in the optional quests, they only exist in the job quests and the MSQ. I know some people hate storyline, but I find the combat storyline bits to be fun, albeit they can only be done once.