This is correct. A lot of the quest hubs are kind of modular, in that you can choose the order in which you do them. And instead of giving you a single achievement for completing all the quests in a zone, we have sub-achievements for completing each story arc. Complete all story arcs in a zone and you'll get the achievement.
What this means is you might sometimes complete a more central or climatic story arc in a zone before finishing all the quest hubs in that zone. That still doesn't mean you should ever be left without a "breadcrumb quest" to take you to the next zone. As far as I recall there isn't a single zone that doesn't have some lead-in quest telling you where to go your first time there.
You'll frequently be given "breadcrumb quests" that lead you to different hubs, sometimes across multiple zones. As an example, when you hit Valley of the Four Winds
, you're pretty quickly given the option to go to either Kun-Lai Summit
or Krasarang Wilds
. It's up to you to choose where to go and what to do first in the valley, Krasarang Wilds
, or Kun-Lai Summit
. If you really want to vary up the scenery and your quest experience, you can even jump around between zones.
That said, as you mentioned there are also some quest hubs that have no "breadcrumb quests" to lead you there. We like the feel of discovering characters out in the world who could use your help, any maybe even unveil some awesome story moments that aren't necessarily integral to the primary story arcs in each zone. They're like little bonuses to give you access to more backstory on Pandaria or the inhabitants and explorers there, and they're also required for the achievements to complete all story arcs in a zone.
To make sure these "isolated" hubs where you aren't expressly sent via a quest aren't totally missed, you'll notice we added new exclamation points on your map to point them out. So while you're questing around a zone, be sure to check your map. Not only will you see where all the flight points are (even ones you haven't discovered yet), you'll see exclamation points at hubs you'll need to find on your own.