Well, I've only run the dump pipe since the turbo was installed (+ two years ago).
Dump Pro's:
Wonderful sound
More power
Dump Con's:
Too much wonderful sound
Right foot/leg smells like exhaust
Basically, it is a sound/noise issue. The dumps at 6am don't exactly make you friends in the neighborhood. Some areas will ticket you for excessive noise. If you are taking a long trip, the sound can wear on you (earplugs are a good idea). I know, you don't normally think of a turbo'd Busa as a good touring bike, but a properly installed/tuned turbo'd Busa (thanks to Frank - Powerhouse) does make a very good daily driver.
The sound forces you to be more aware of your environment (neighbors, police, etc.)
I have entertained the idea of getting a pipe, and then, since I'd have both a pipe and the dumps (with both maps), I could put on the pipe or the dump depending upon if I wanted to go on a long trip, or just enjoy myself. At this point, I'm not sure if it would be worth the money (~$800 for pipe and map). For that money, you are getting close to intercooler range...
Good luck.