Pros: It's very versatile and you can adjust about any parameters you want to with it.
Cons: The biggest is that the learning curve is VERY steep. Make sure you are ready to commit mucho time to learning to tune before you make the final decision. It's also more expensive than the handhelds.
Personal opinion: If you just want to get rid of sluggish takeoff, your best option is to buy a 2600 stall converter like a Yank TT2600 and have the shifting adjusted to account for the converter. You can do that with a handheld tuner if you want. The converter made a huge difference in off-the-line performance on my truck. If I had put the converter on before the supercharger I might never have started down this never-ending path!
I have HP tuners and could not agree with MyBigToy any more, he is spot on. Its great when you figure it out, but will take a long time to do so and not worth it for just a mod or two. If you dont do your research and just start adjusting stuff your motor and/or tranny will be toast in no time.