Some can tie into the main scenario. But to tie all of them in and you run the risk of becoming "tedious". Bioware had eight writers, one for each class. If you were a gameflow junky, too much story/cutscene becomes a hinderance. XIII received a bit of critism on that front.
They did a terrible job at it though. It wasn't the class quests that were repetitive or redundant, it was more of the fact that you had to traverse boring planets like Hoth or Tatooine that were largely uninhabited while doing quests with trivial objectives.
Case in point:
"Master Jedi! I need space rope!"
(Run a million miles in one direction, collect space rope, run back, next task)
This sort of questing is boring and TOR suffered for it, particularly when you got to daily quests. I wouldn't want to see the same fate fall upon 14. They can absolutely pull off this feat; just make quests remotely meaningful to the overall feel of what's going on in the world.