So when I was there back in January, all the information they had posted said that the Tower would house the new lobby (and that was confirmed by CMs). I do believe that it planned to have a bus stop there as well, but it never said if the preferred rooms would be moving/they would be relocating the bus stop right in front of the current lobby/food court building.
I don't think you'd be in a bad transportation location if you chose either. I was in a preferred room in Casitas 4 and enjoyed the short walk to the food court/current bus stop. There will be a lot of amenities in the Tower and it was maybe an extra 2-3 minutes to walk over to the tower location (or at least as far as I could go, but it wasn't a direct route).