Shorty's are an easy bolt on part, whereas longtubes require lifting the motor up and make starters a bitch to get at. Having said that, shorty's will likely lose you a little low end on a stock motor and you probably won't notice anything other than exhaust tone. Longtubes create more power all accross the RPM range and sound better to boot.
Shorty's are a waste of time, because you'll probably go LT's down the road anyways.