In the Expansion Main Story..

[Violyre]

Yes, however, in between you had to do other pointless thing like 6-8 quests involved Bacchus' Wine before you could even do Titan Story. Could skip all of that pointless "back story" ( which can be told in a side quest).

In Ala Mhigo, You had to get the leader of the base your trust but he wouldn't have it, so you had to go Quarrymill and do 8 or so quests before he sends you back to little Ala Mhigo with a letter of recommendation.

Both of those had good reasons, as both were made of a "why should I trust you?" thing. The CoH didn't want to send some idiot to certain death. The Ala Mhigo have no reason to trust anyone but themselves after how they were treated when the fled the Garlians.

Would you rather it go like this?:

"Why should I trust you?"
"I'm an adventurer."
"Okay I trust you fully."

The other thing the missions did for you was guide you along one path of leveling you could do.