I have mixed feelings about most questlines that weren't really job quests. WHM and PLD come to mind, it would've made very little difference if you were a CNJ or GLA.
Favorite questlines... BLM always hits close to home because of how well it fits my chara's rp story, and the fleshed out lore regarding our relic weapon was a very nice touch indeed. On broader story strokes, DRK was amazing but there were a couple of contradiction with the 30-50 questlines that rubbed me off the wrong way. That's why SMN gets my vote as best, I love how close its plot is to a lot of things that don't necessarily affect the MSQ currently but are in the midst of the world's lore, like Ascians or Allag. Next one worth mentioning imo is MCH, it always feels relevant.