Ability to really fix up settlements that come with a good amount of (mostly) intact buildings. Really frustrating for the settlement-builder part of me to try and cover glaring holes in walls/floors, and can only ad-hoc coverings, making it look really ugly and sometimes still leaving enough of a gap that myself/npc's might fall thru the floor if we are not careful). So if you have the raw materials to spend, pre-war buildings can be fixed up to be practically new.. no more nasty holes in the walls, floors, ect.
More powerful weapon/armor mods. (we end up being the biggest mofo in the commonwealth..we should severely out-gun pretty much anything out there right now, with master-level perks and high enough character level)
More stuff to build in settlements (furniture, decorations, functionality pieces, ect)
Being able to see what your settlers are assigned too, so you dont accidentally take somebody off of food production when you assign them as a shopkeeper or supply-line worker
Companions go with you into the institute, and dialogue (maybe a quest or 2) that results from it. Can you imagine the fit piper would throw if she made it in?
A meaningful under-water area. Maybe a secret research installation, military base, under-water vault, or even an alien base.
Kitties in settlements
Radio tracks in the loot tables, that you can bring to the diamond city Dj as quest turn-ins, as well as for your own radio's in settlements
Stop letting preston / the MM treat us like their own personal lackey after we make general. We have grunts to take care of the day-to-day settlement concerns (no more endless radiant quests, plox)
Plug those breeches in the castle walls after we take over.
A more varied enemy list
A couple -really- big settlement sites. I mean BIG. Would be nice to really tinker around with stuff, maybe make a large town (as opposed to the very small sites we get now)
Give us build-able robots as part of the defense force. Tired of the gunners always getting the assault-trons