I'm sure someone will correct me if I'm wrong but isn't it the story from the VFX people that the ship was designed to be pretty much the same scale as the original and then well into production they realized that it needed to be significantly bigger to accommodate the shuttle bay, engineering, etc. and so they just scaled down the windows and that side docking port (at least it used to be a docking port, apparently now it's a recalcitrant crewman ejection tube) and didn't bother to add more windows so that it would look like there were more decks?
The choice to make the windows larger instead of more numerous was a deliberate one. In
Star Trek: The Art of the Movie there is this concept illustration of the Enterprise with more, and smaller, windows:
Deliberate, how? Do they say? I've never been a fan of having the outside of the ship littered with windows, but when you keep the same number of windows in the same place and just make the ship bigger, it suggests a certain... laziness. Or lack of time (which would suggest poor planning or preparation).
Again, while I'd have preferred a ship the same size as the original, I don't mind that they've made it bigger. I just think they were sloppy in how they went about it.