I've been going through Costco for so long, I'm a little biased. A con would be that you can't choose the person with whom you talk to each time. You must call the 800 #, and its the luck of the draw. I've had some really great interactions, but I've had a few that were not so great. There are times when I feel that I'm having to direct them as opposed to the other way around. When you choose a non-Costco TA, you can choose a specific person (from recommendations, etc), so at least you'd be dealing with the same person all the time.
Another "con" would be if your local Costco won't cash in your cash card. You'd be forced to spend the funds in store.
You can only pay with Visa or MC on the Costco site (many people open a Disney Vacation Account and pay with that - you get a bonus on spending from the account + you can load Disney gift cards purchased at a discount to your DVA).
Also, I believe if you downgrade your room, they are supposed to charge a small fee (I've never done this, so I can't say how much and whether it is enforced).
One thing to note . . . if you see a room thats available on the
DCL site, and you call Costco to book, sometimes that room is in some kind of cyber limbo since you just accessed it. I've had Costco agents insist that the room isn't available to book. I've had to ask them to call DCL to verify. DCL can then work their magic so that Costco can grab the room. Or just be patient and wait for the room to come out of cyber limbo.