You have a ton of options with that vehicle. A lot depends on what your final goal is. Do you want an SQ (Sound Quality) system or a bumpin' SPL (Sound Pressure Level) system? Or do you fall somewhere in between? I personally am building an SQ oriented system that will also crank up loud without losing any of the quality. Of course that put me in a whole other budget level (think stupidly expensive).
What kind of music do you like? How loud do you like to play it? Are you looking at a component set or just the best options for the factory locations?
What I would do is try to plan your whole system before you buy anything. I would try upgrading the head unit and adding a 4 channel power amp to the stock speakers first. This will improve the overall sound quite a bit. Then you can decide whether you want a sub or new speakers next. Then finally finish off your system in the last stage.
Jl Audio makes a couple of completely stealth center console sub boxes for your vehicle. They are not cheap but they are completely invisible and you will not lose any interior space.
If you upgrade your head unit with Alpine (I'm getting the 9835) make sure it is one of the models with the V-Power amp built in. They are the best sounding and most powerful integrated amps I have seen in any head unit. You could just start with that wired into your stock speakers and see how you like it. Then, instead of getting an amp and new speakers for your doors, you could get the sub and amp next.
If you want to learn a lot, go to
Elite Car Audio Forums and just read. Use the search function to figure out any terms you don't understand. After you've done some reading you can ask questions over there. I would say they are the equivalent of HTF when it comes to car audio.
Wow this got long. . .
Answering the first few questions will help you in designing your system.
Tom