I think these are all great ideas and it seems to me that these would all be achievable as DLC because all of those things you described are in the game at different points, but most interior stages aren't available outside of the specific mission, even though they could be available. Theoretically. I admit in my ignorance I might be underestimating how difficult or time-consuming these implementations would be, but — these assets are already in the game. The code is written. Even just being able to visit the museum Mary Jane's mission was in as Peter or Spidey, or Norman Osborn's penthouse, or some of the sewer areas or other base token stages — in the post game at least, why not open up the areas have a timer for a transition effect into a new day cycle and weather cycle, etc?
It just needs to be connected and opened up, somehow, and it'd be close to perfect.