I'd love some kind of utility where you install the mods you want, run the patcher and select which menus you want from the mods. Want the walls from Homemaker and Better Settlement Buildings? Check.Want them sorted by small and large? Check. Don't want the cars or raider stuff? Don't check. Want Snap'n''Build or Alternate Settlements in their own menus? Check. You'd choose which menus you want and maybe how you want them.

I don't know if it is possible but it would be a solution for the menu problem.