Booking individually gives many advantages... First, many hotels are cheaper when you book directly. For instance, if you call Park Vue Inn for a reservation, they will knock off a bit of the price of their rooms (in my experience, about $10-20/night, but it's been as high as $40/night off when I mentioned we were returning guests). Along with booking directly, there's some hotels on Harbor that aren't Good Neighbor hotels (again, Park Vue), so they won't even show up as an option on the .com site. I'll come back to the Good Neighbor designation in a second. Back to booking directly--lower prices from the hotel, and a larger selection of hotels. It also allows you to find lower prices on tickets. For example, some corporations participate in Tickets At Work, or Life Balance Program, which provide
discount tickets. Last Minute Travel and many other sites also have discounted tickets. 3+day tickets with park hoppers will usually have Magic Morning on them--if they are bought at the gates, or are Military Salute tickets, they won't have MM, but almost all others do. It's nothing "special"/extra that you get from buying the tickets directly through Disney... However, ALWAYS buy through a reputable 3rd party seller, not someone off Craigslist
So, you can save some money booking the hotel yourself, and an additional $20+ per ticket.
Benefits for booking through Disney? Oh, you get the luggage tags! And some coupons. I think sometimes you can get PhotoPass for "free" with some packages (or you can pay $10/day for MaxPass which has PhotoPass, and still come out ahead of what you would otherwise spend in the package). I think you may still get the plastic "souvenir" entry cards, but I'm not sure about that--I feel like I remember hearing that they started sending the cardstock tickets.
Good Neighbor Hotels. Disney says, "Hey, give us $$$, and let us sell a few of your rooms for your hotel and we'll give you the title of Good Neighbor property! Then you can sell your customers tickets to our park!" And the hotel says, "Oh, okay! Here's $$$, and number of rooms you wanted. Thanks! We'll recommend all our customers buy your tickets through us!" There's no quality measures, no cleanliness requirements, no maximum distance from the parks, no extra Disney features the hotel gets (other than the ability to sell tickets). Sorry, I take that back... It allows the hotel to buy certain promotional items, like flags to hang on their property. So, Good Neighbor hotels are fine... but they aren't any better than any other hotel.
