I had some topic with a few ideas before, but none answered, so I don't know if everyone is happy or don't care, so I will post it here again:
Generally I wanted every main faction to be more focused on only some types of buildings and more of them non combat, but more about what makes the factions different.
For BoS I was thinking about factories - that you would
Spoiler not only search every building
, but factory for some pre-war relic, but also you should discover what that factory was producing and get schemes and even construct some parts right there.
I still didn't play really BoS-I couldn't get over the starting radiant quests, so I don't know what is there really.
For Railroad I wanted more of subterfuge /camouflage quests, with larger net of hideouts, where you could do small quests for each of them.
Spoiler And the quests with MILA could really lead to interesting high locations, not only some roofs.
For Minutemen I would like to have 1 interesting starting quests like it is in Finch farm, The Slog and Greygarden.
And I think they are maybe the only one that have some real influence over the world, I don't even have random quests from them, or I fail them, so still they are OK for me.
Spoiler But I wish they would be connected more in conflict with Raiders, because they seems to me like the opposite, the same way Railroad/the Institute is.
I still didn't do Institute, but I wish it would be a lot about experiementing myself, entering all vaults with missing info about them and to do some important quests, that would reveal more about this secretive organisation.
Generally I wish there would be ranks with rank 1 with only 1-2 generic /combat quest line, before you would get promoted and moved to more important half combat quests. And 3rd rank would be working on top secret mission.
It is a bit of there when it starts, but I'm not happy with the filler quests