LBRB45,
If you don't shoot very much it doesn't matter. Many old skeet shooters who are experienced with over/unders will tell you that because of the stacked barrels, an o/u has an invisible fulcrum. This causes the bottom barrel to lever the stock into the cheek, and the top barrel to lever it away from it.
In the course of a long shooting day (several hundred rounds), this upward levering can get a bit painful for some people. To reduce this, most of us used the top barrel for the single targets. For this reason,trap shooters who shoot o/u's also often shoot the top barrel for singles.
John,
Rotating barrels to even the wear is nonsense. The first place to wear in a quality o/u is the hinge pin and locking lug. And that takes many, many, many rounds.