We just returned and stayed at two different hotels (stayed in SD day before and day after our cruise). We quite liked the Comfort Inn (there are two) in hotel circle. We ended up getting dropped off at the wrong hotel but that was okay. We didn't go to any parks that day but I don't think that there was a free shuttle to Sea World or any park. It was a suite so there was a kitchen so if you're staying long that is a good deal and the continental breakfast was pretty impressive as you get to make your own waffles. we also stayed at the super 8. it was about the same price as the Comfort Inn but the room was not impressive. While there was a free shuttle to sea world it wasn't great for the price in my opinion.
Hope that helps??