I've been going to WDW for just about forever (well, since I first went during the soft opening in September 1972, before they even officially opened the Magic Kingdom, I guess it HAS been forever!), and am very much usually a hands-on kind of guy. That said, I've booked over the years through Disney directly, through a "regular"
travel agency, and the last 2 times through Disney Expert travel agencies (I won't name either of them so as not to in any way seem to be pushing them over
Dreams Unlimited who is a sponsor here on the Dis; I've never used Dreams Unlimited and so can't say anything about them good or bad).
Back in the "old days", I used to book exclusively direct with Disney. Then I tried with a regular "general" travel agency. BIG mistake, one that I don't plan to ever repeat again. A mistake only because they knew far less about WDW than I did, and could only seem to figure out how to book the most expensive possible rates, not necessarily even what I "really" wanted.
The last two times (Oct 06 much-too-delayed hunnymoon trip, and our upcoming return to WDW late Sept to early Oct 07) I booked with 2 different Disney expert travel agencies. The 06 trip, the agent I used was "fair" though nothing spectacular one way or the other. The agency is well known and did come well recommended, but, I didn't feel much like I wouldn't have done probably just as well if I'd have taken the time to book it myself. The 07 trip, however, is a whole other story....
First, for the 07 trip, we hadn't even planned to make an 07 trip. Still, I'm addicted to all things Disney (like so many of the rest of you, I'm sure), so one of the various things that I've gotten into the (bad) habit of doing is that I occasionally check out the different travel agencies & see if they have anything special to say, "just in case". Well, the 07 agency had a special rate for the time that I COULD take off, and the rate was good enough to make me decide that we WOULD take off & go down. It's my wife's birthday, so I wanted to make it extra special. So, while our hunnymoon was only a Tuesday-Sunday stay, this time, we're going to be at WDW from Saturday through until the following Sunday (yes, we get in mid afternoon on Saturday, thanks to the airline changing our flight time, but still, not so bad). This agency had rates that I found to be MUCH better than both rack rate & what other agencies were offering, both for the rooms & for tickets too when purchased as one of their "packages".
I've also been in touch with the agent I now have assigned (had a few problems with the original agent as she was having a personal emergency at her end, so she was VERY REASONABLY unable to respond in as timely a manner as I felt I needed) and we've talked about what options we are/aren't willing to consider if they come up (if they extend
free dining, if they come out with AP rates, etc). She also offered to make all of our ADRs for us if we wanted, but, because we've been still figuring some of this out, I've opted to handle the ADRs myself so that I can juggle things as needed.
So, what's the moral of the story? Disney will get you what you ask for, but, you have to be VERY sure to ask for any discounts, sometimes even "leading" them to your discounts. A general travel agency will book you a general stay at WDW, but probably won't give you anything special, and may well even cost you more in the long run than going direct with Disney. BUT, if you go with a GOOD Disney specialty travel agency, you can sometimes get some EXCELLENT deals and get some of the most valuable assistance you're going to find. They tend to check for changes/additional discounts daily, so that as things come up, they'll contact you & suggest possible alternatives that either might save you money or might make things closer to "just" how you want them.
Whatever you do, Enjoy the Magic!
Forgot to mention, I don't work for Disney or any travel agency, nor am I connected in any way to them. This is just my own opinions and as always, Your Mileage May Vary.