A couple of years ago we held a VERY long discussion on RCC, with people citing actual chassis dyno numbers and quarter mile ETs, as well as some fluid dynamics input from the egghead engineers amongst us, and a briefing on reversion wave exhaust tuning from me. I think the thread got lost in the server change, but the result was:
Headers "Yed" into a single 3 inch, with a 3 inch high flow cat and Dynamax (or similar) muffler will give you a bit better performance and mileage than two 2.5s. Do the math on the flow capacity (volumn of a circle versus the internal surface area), and you'll see why. The main reason for one large single is the ease of routing the pipe.
The slickest set of true duals I've ever seen were paralleled down the same path that the factory single runs, with dual high flow cats, then a long low angle 2.5 inch diameter "X" pipe in line near the trans/transfer case, and the mufflers staggered one behind the other so the system would take up less space. Sounded great and ran good. Was expensive ~$600 complete and installed. Passed Smog test.