The pricing can vary--look at it both ways. However, if there are any specials offered, you have to book separately to get them. For instance, you can't get free dining on the land/sea. We were able to book a bounceback cruise special and a WDW free dining special by booking separately.
Also, booking separately gives you A LOT more flexibility to get what you want. You might want a balcony on the ship but are happy in a Value resort on land--can't do that on the package!
Every part of the package can be purchased separately, and might save you a lot of money!