The "happy medium" in exhaust piping size is something we generally always try and find when it comes to vehicles. Finding a good pipe size where there is enough back pressure from the atmosphere, but also enough room for the exhaust to flow out unrestricted is tough with some vehicles. However, jeep got it pretty damn good putting 2.25 diameter piping on our 97 jeeps, and the intake is also pretty unrestrictive stock. Some vehicles benefit much more from CAI and aftermarket exhaust systems because the stock ones were restrictive, but this is not the case with our wranglers. Your best bet is to find an exhaust system that maintains that 2.25 diameter piping.
Anything smaller is going to be too restrictive and make the engine work harder to push the exhaust fumes through, and anything bigger will cause a loss of the backpressure krisbman alluded too.