Since Bethesda does not "finish" a game anymore before release since Skyrim, and instead adds features with updates I hope some of the below will make it into the game.
Weapon(s) visibly holstered on the body. There shouldn't be a clipping problem when scripted in such a way as to auto-remove it when entering PA.
Closing and reopening vault doors should not have been removed, this is just a laziness. Also it makes no sense that Vault 87 becomes an open house as soon as I promise 3 fusion cores to the overseer and it never gets closed behind me.
Sea monsters, unless provided in an upcoming dlc, why are there no mutated dolphins/other animals in the water and cut out of the game?
When a location is reset please do not place the damn protectrons in their holding tubes again as it breaks immersion.
It is a short list for now, maybe others got better ideas I'v missed?