I feel as though I am in a good position to help you here, as I am travelling to WDW in November 2013 on a flight inclusive package with Disney and have booked other trips, flights and hotel separately:
For my November 2013 trip, I booked the hotel/ticket element of my package very very early (May 2012). Ever since, I have been comparing prices both with WDW and other providers and found that by booking early I obtained the best discount possible and got free dining and a $200 gift card to boot. I was very happy with this and could not find a cheaper way.
Anyway, in December 2012 my direct flights were released. Disney allows you to upgrade to a package holiday when this happens with no amendment fee. Disney quoted me around £150 more per person for the direct flights than the cheapest provider (the airline themselves) could. This was where I could have saved myself a few quid. If I had chosen to fly indirectly (which I personally hate doing) I could have saved around £250 per person. As there are only 2 of us travelling, I decided to go for the convenience and security of having my booking all in one place.
To my dismay, I also later found out later one of the cashback sites offer cashback on holidays booked with WDW (around 3%) so that would have saved me even more!
The last time I booked my holiday separately was in June 2008. I booked this holiday really late (around 6 weeks prior to travel!) This time, I booked the hotel/tickets direct with Disney (they were the cheapest at the time) and managed to get flights to Sanford from Manchester (chartered) for £255 per person return! I never expect to get flights that cheap again!
Anyway, my point is, if you are clever with your booking (book early, use cashback site etc,) I think in terms of accommodation and tickets (assuming you want to stay on WDW, booking direct with them will always be your cheapest option. Flights on the other hand can vary in price so much. If you are prepared to fly indirect this is definitely the cheapest option (in my experience potentially to the tune of around £250 per person) or if you are also prepared to "DIY" this could result in further savings.
Personally, I would always book a flight inclusive package direct with WDW. I know it is more expensive, but it does give you peace of mind, such as full ATOL protection, as well as the ability to secure your holiday for only £300 (airlines want payment for flights upfront!)
Anyway, good luck with whatever you decide to do and I hope you get a deal with which you are happy!