Lots of great information here:
www.disboards.com/threads/choosing-the-right-hotel-for-you.3656512/.
Also, would a suite work just as well as two separate rooms? Or would two connecting rooms work better? There are all suite hotels now (some quite new) on or very near Harbor. Check the Springhill Suites, Residence Inn Convention Center (this one is newer) and RI Main Gate (this one is older, but has great staff), Homewood Suites (right by the Toy Story lot so you could take the free shuttles), etc. For two connecting rooms, we like two premium rooms at the Candy Cane Inn. The premium rooms are larger, come with a small refrigerator and microwave, DVD player (free DVD rentals at the front desk), bathrobes, amenities basket, breakfast delivered to the room (a big help in the morning!). CCI has a private shuttle that runs on time and is also walking distance to the parks (about 10-15 minutes depending on how fast you walk).