Honestly, it depends on how much of an audio-affecionado you are. To me it seems as if you are probably mildly to slightly moderate in your level of expectations from an audio system. With this knowledge in mind, I would say the factory Bazooka sub would be just fine. People tend to get mislead with the sub as it comes from the factory turned all the way up, which obviously does not lend itself well to "blending" with the stock speakers.
With a little fine tuning of the "gain" on the built-in amp, I would say the sub would provide enough mid/low frequency output to suit your needs and wants in an audio system. An aftermarket hookup will only prove itself cumbersome to you as it takes up trunk space and is prone to different types of malfunctions. Do yourself a favore and go the "seamless" and problem free route of letting the dealer install the bazooka, that way if there are any problems, you wont have the headache of dealing with the 17yr olds at Best Buy who will focus more on "pimping" your car for the day instead of installing your system. - t