I think the most important question you have to ask yourself is: how long are you planning to keep the car? If you're in it for the long haul, it would be best to find a reputable shop and have your car professionally tuned. My local tuner of choice (IAG Performance) protunes using the AP, so I ended up needing it anyway. Your car will run optimally and last longer, as long as you don't abuse it too bad and keep up with maintenance. If, however, you're only going to keep it for a couple of years, go with the AP and flash an off the shelf Stage 2 map on it. It's easily reversable and you'll be able to sell everything and recover a good bit if your money (APs tend to hold their value rather well).
Another question you should ask yourself is: will you stop at Stage 2 or modify your car further? If you're just going to stop at Stage 2 (due to family, financial, or other reasons), an AP would be good, but a protune would be better. If you're going to modify beyond Stage 2, you'll need a protune eventually, so the AP should suffice until you collect and install the parts necessary to support an upgraded turbo.
I remember struggling with that decision several years ago. I initially went with the AP and an OTS map because it was very important to me to be able to revert back to stock completely if I had any warranty issues that required a trip to the dealership or had to sell the car (stock cars are generally worth more than lightly modified cars). The dealers can see if the ECU was altered, so I probably would have lost that battle anyway. Odds are that nothing will happen in the first few years of ownership, but it still gave me peace of mind. When my car was finally paid off, I got a protune and went a bit crazy with the modding, but that's another story