Michael pretty much nailed it. When it comes to mechanical simplicity, balance, safety, reliability, and generally speaking; ease in target acquisition and follow through, a O/U is pretty hard to beat.
When you consider you're only shooting 2 targets at each station, the O/U gives you all you need, ease in reloading,and you always know how many rounds are in your gun.
A lot of guys at the skeet and trap clubs, as well as the sporting clays course, are using auto's more and more. Probably largely due to the easing in felt recoil. You can shoot a Benelli or Beretta auto all day, even with the hottest trap loads, and you'll hardly feel a thing.
I've got a Beretta 391, in addition to my pump action guns, and personally prefer autos. But there are a lot of fine O/U's out there and they're not all over $2000. The suggestion to look at the Ruger Red Label is a good one. Some guys think they're a little heavy, but I don't. I don't mind a little heft in my gun, makes for easier follow through among other things, IMHO. Also, look for the Franchi Alcione. Fairly inexpensive (under $1000) and has a transferable barrel system allowing you to have 20 ga. and a 12 ga., essentially. You can also find some good deals on used Beretta 686's and Browning Citori's from time to time.
