Because Disney doesn't release their promotions very far in advance, I've been very wary of booking any Disney packages through travelocity or orbitz. It seems that you save a few dollars that way but the reservations aren't adjustable if a promotion is released. My understanding is that you have to cancel the reservation - which might incur a fee - and rebook.
Travel agencies that book directly with Disney have access to all of the Disney promotions. We've used "Build A Better Mouse Trip" - which only does Disney travel - and they've kept us updated on special promotions. We've actually had our package cost go down. They've done a good job of helping us figure out what we actually need: Is the Water Park, Fun & More option a good value or are we better off with single day admissions? Do we need the park hopper option? Do we want the insurance? What type of room do we want? Etc.
I've also booked directly with Disney and it seems to be fine if you know exactly what you want. Their system seems to default to the highest price option on tickets, rooms, and insurance. People who enjoy researching probably do just fine but I suspect that the average person who just calls Disney ends up paying for features they might not need or use.