Cost-wise, there is pretty much no difference between booking through a TA and booking directly through
DCL. Many TAs will give you some sort of incentive to book through them. Disney-certified TAs (like
www.dreamsunlimitedtravel.com or
www.smallworldvacations.com) will offer on-board credit (OBC). I know Costco had a deal going where you'd get a Costco gift certificate or some such. Another TA offers a bunch of frequent flier miles.
The big advantage to booking directly is that you can make changes at will. If you book through a TA, your TA has to make those changes on your behalf. Personally, I book through a TA in order to get the OBC. Additionally, DCL keeps track of which
travel agency you used, so if you want to re-book on board, they can re-book under your travel agency, and you should get any resulting bonuses from that. But do check with your TA about that.
One other thing to be aware of: if you shop around, you're going to see lots of different ways of seeing exactly the same information presented. Let's take the Feb 2, 2013 Fantasy as an example. On
www.skymilescruises.com, they're advertising "Balcony as low as $1673". On disneycruise.disney.go.com, verandah staterooms start $3547.56 for 2 people, and they specify Cat 4A. Why the discrepancy?
Digging deeper, on the DCL site you see they charge each guest $1701, and they add $145.56 for taxes and fees. If you go far enough into the skymilescruises process, you'll see they're also offering Cat4A, and when you drill down to the pricing, what's available is $1701 per person plus $72.78 per person in taxes, for a grand total of $3547.56.
The only difference is you get a couple thousand miles added to your frequent flier card if you go with skymilescruises.