How about the lack of towns. Salem, University Point, Quincy could of all easily been open towns instead of just another mob filled area. Also the Minuteman quest line could of been much longer where we help all the non existing towns out while building small farms and settlements. Doing so we'd encounter Kellogg and maybe some Coursers that we wouldn't be able to kill at places such as the fishery and University Point. Eventually after saving the townfolk of Quincy they would let us into Diamond City (rather then just letting us in 5 minutes into the game), find Nick then go on the true hunt for Kellogg. So a proper Minuteman story line capping off where we've helped and built a decent amount of towns building the Minuteman's power. Then we get lead into the second half of the game of finding the Institute and the war between them and the Railroad/Brotherhood/potentially Minuteman. Also proper towns which would have their owns quests and such... Take it even further and allow an evil route where we betray the Minuteman at Quincy for the Gunners. We then use the Gunners to take over all the land we claimed as the Minuteman. After the Institute attacks Green Tec we find our way into the Institute but Father is all 'you are to corrupted go away'. Will stop now as the idea train has started but cannot go anywhere for now....