I'd rather have complex outcomes and meaningful decisions over tons of options min/maxing my character to bypass skills not needed for my character build. So I actually don't mind the streamlining of skills and annoyances like weapon repair. Even characters flagged as "essential" is something I can tolerate. What I don't like is how NPCs in Bethesda RPGs all seem to treat you like the scum of the earth no matter what your accomplishments are, and there is nothing you can do about it outside of installing mods. The world in Bethesda games should react to your actions, good, bad, neutral or mixed.
Fallout definitely needs branching quest lines and consequences. Especially for side quests. One of Bethesda downfalls is they do not truly allow you to play an evil character, just being a jerk for the fun of it and have certain people react accordingly. I might want to be a Sole Survivor who says "[censored] everybody, I just lost my family, this world needs cleansing". I should have a choice to play out a character like that until the end if I don't have a change of heart.
All in all, I'm happy with Fallout 4 despite it's flaws. I just hope Bethesda ramps up the difficulty for the Very Hard mode for people who want the Survival challenge without worrying about food, water and sleep.
Off topic, there should be a way to destroy the MInutemen.