Mommo,
Historically, in most cases it's cheaper to book the components of your vacation seperately (room, tickets, etc.). This is particularly been true if you can get ahold of an AP discount or a room only discount code. Up until FTP was unveiled, you basically paid full prices for everything when you purchased a package via WDW. The only "savings" you got was only having to make one phone call to set up your Disney vacation.
However, after FTP was rolled out, Disney seems to be cutting back on the AP and room only discounts and starting to lean towards packages that contain actual discounts. When the AP rates for the latest season were announced, it seemed that most of the rooms were gone in a couple of hours after their release. Last year the AP rates for the Jan value season were released just before Halloween, so the next week will be telling.