I really don't think it is a "hard choice" when it comes to the MQ. Think all sythns should be destroyed? Join the BoS. Think Sythns should be free? Join the RR. Agree with the Institute? Join them. Prefer a more good guy approach? Join the Minutemen.
Is there a single consequence in FO 4 like the Roy/Tennpenny tower quest in FO 3? Is there a failure state to the game besides your character death?
Are there any consequences to SPECIAL? I don't see any, there are zero dialogue options based upon Special that I have encountered, every persuasion attempt only governed by Charisma(with a unknown % bonus based on black widow or lady killer), no INT checks for dialogue etc, and this was even in FO 3. I took a pretty crappy SPECIAL loadout, basically just "average" in everything, and I've had no problems in the game. Dialogue choices tend to lead to the exact same outcome.
Really, where are the big consequences that down the road change the game? I've had some triggermen come after me, that is it. What are the evil choices? Seems like the only evil choice would be to go around and just refuse to help people or something.
I like the game, but they dropped the ball on lore and C&C. It is better than 3. There doesn't have to be groundbreaking C&C with every quest or around every corner, but a taste of it would be nice.