Well, that is the problem.
"Be who you want, do what you want"
But that becomes less and less so with each part of the series.
It becomes more linear and forced.
Oh, come on now. I'll use both examples here-
A thing called "X" is in that dungeon. You need to get it to accomplish a needed task. Yeah, it IS forced- you need it to complete the task! You can't make an iron dagger without leather strips and an iron ingot, either, right? In these cases, the only choices ARE- "you can or you can't"
People in a guild have info and input you need. To gain access to them, you must join that guild. Yup, forced again, and it makes perfect sense, just like you can't get Legion quests without joining the legion!
What choices do you feel there should be? Wait for another hero to get the item or knowledge, and then win that item or knowledge in a tic-tac-toe contest? Or maybe rock paper scissors? Be reasonable here. That has nothing at all to do with "be who you want, do what you want". A quest is a quest is a quest. If you want to finish the quest you do what is required. That's why it's a "Quest". You can either succeed or fail.