I'm another Disney Dad that has found the same thing. In fact, it's very simple to do some detective work on disney.com and price out variations and such and figure out prices for different parts of the package. For example, you can check three nights at any WDW resort, and then price the same thing with Ultimate Park Hopper tickets and figure out the package price for tickets. Taking into certain considerations, of course....same thing with Disney's prices on airfare. At times, I've actually seen fairly reasonable prices on airfares in a package (not so much reasonable compared to an airline like southwest.com, however, an airline that actually allows seat assignments ahead of time, which is worth a differential over southwest, in my opinion).
Here's my pet peeve, though...say you want to book a multi night stay at a WDW resort. For someone like me, flying in from out of town, I can't really be there that early the first morning. I get a half day or less at the theme parks. Same thing the morning that I leave...maybe I get a half day. However, in both cases the package has charged me for full-days at resorts. In fact, with the online reservations, you can't "unbundle" at all in hopes of saving paying for tickets on a day that you can't get to the parks (which might be the case if you have a very late flight coming in, or an early flight leaving).
On our very first trip to WDW, circa 5/95, my wife and I arrive very late to CBR. Around 11:40pm. In this case, when making the reservations, I had figured out that I needed to ask the reservations person for one day less on park tickets (six days of park ticketing for a 7-night stay). As the front desk guy handed us our package, and key cards, he said something like "and here's your cards, which are valid for park admissions starting right now." I asked him "for the next 20 minutes?" It was much trouble, but he reticketed us.
Lately, with two adults and two kids, those theme park tickets prices really add up for us, as they do for all families that go to theme parks. If one is really on a budget, staying at the All-Stars, for example, with package pricing, those theme park ticket prices can far outweigh the price of lodging.
So, I think it makes sense for the buyer to become educated...try pricing things out, asking questions and such, and don't automatically assume that package pricing is giving any sort of a break whatsoever. It most likely isn't.
Guy