Heh.. if that's the case you should fire your tuner... Seriously, a lot of bottom end can be woken up with a proper tune. Especially on the 2.5 liter cars.
The AP also comes with support from Cobb, tuning software if you choose to dl it and also has some other nice functions that make it useful. Bottom line is its just an interface in which you can tune with. That said however, there are other ways to skin the tuning cat. Open source is always an alternative that many people have had great success with. I've been happy using my AP and ATR software to tune.
Correct

As stated, cobbs maps are very conservative and are tested thoroughly to make sure they're not liable to damage your car. HOWEVER.. you really should data log ANY tune you flash onto the car. Another thing to remember is that immediately after you flash the car, the full timing advance has not come into play yet and it WILL feel weird for a day or so until it "re-learns".
Dont be affraid of E-tuning either. As mentioned (Torqued Performance) and other vendors can give you a base map and make adjustments from datalogs that you send them. This method is pretty effective and doesn't require you to actually go to or pay for Dyno time. Both AP and Open Source have a following of tuners that will do this for you.
My suggestion is to get the AP and flash Stage I .. see how you like it. If you want more, do some more reading and/or call some vendors and see what options will work best for what you want out of the car.