1 - I'd favor Dogmeat getting his own follower slot - but not infinite followers. I didn't really care for it in Skyrim, because a squad could make things too easy, or just gum up your path. The idea of having a good squad for battles is appealing, but I haven't had much fun with it in Bethesda games.
2 - I'd like to see more dynamic recruiting. Find settlers with skills - if you build it, they will come. Traders show up if you build trading posts and the like. I'd also love to be able to recruit/train Minutemen. Perhaps all they can do is defend a settlement when trained (so you have to leave some settlers as farmers).
4 - I would like to see an inventory system that marks 'new' additions to inventory. Quickly find what you're looking for. Also, I think you can auto play holotapes - I ran into one today and I pressed R to pick it up - immediately loaded it into the Pip-Boy.
5 - Or an auto scrapper - what else am I going to do with those 9 tin cans I disarmed?
6 - I think Super Mutants have always been fast - I recall getting rushed down a lot in FNV.
I'm not expecting anyone to drop what they're doing and make these - I don't know how to mod (although I'm interested in giving it a shot this time around), just some things I would have liked to see Bethesda put into the game.
Many of the things I want to see as mods spawn from a "why did Bethesda decide to do it THAT way?" mindset.