Way to jump on the new kid and sell him some bullshit. A MSBassPro "That's engineered on every level"? LMAOSince you don't have the car yet you're going to want to decide if you want the Sync premium sound system. I don't have much experience with it but I can imagine it would help the resale value. The days of popping in a new head unit like it's mandatory are over. I would try a nice line out converter into a 4-channel amplifier on the stock speakers and add a small ported subwoofer system with a level adjustment knob to put in the dash.
There are some good options out there for a high quality LOC. The one I'd go with is the Cache COE6. Then I'd run a Precision Power P900.4 for the speakers. JBL MS-62C components fit into the stock locations. JBL P662 coaxials for the rear or use that money to improving the installation. By improving the installation I would put money into sound deadening. At least put on some vibration damper around the speakers and in the trunk where needed. You don't need to cover everything but just use good product selectively. My preferred vibration damper is Alpha Damp. It's currently on sale for 50% off at diyma.com.
A new product that I hope gains traction is the JBL MSBassPro SQ. This is a self-powered bass enclosure that's engineered on every level so the components perfectly compliment each other. It's about 2 feet wide by 1 foot tall and 1 foot deep so it doesn't take up much trunk space. It's also easy on your alternator but it puts out a hell of a lot of bass for only 300W RMS. I installed one in a Civic sedan for personal friends who are constantly listening to music and they love the sound quality.
Once you figure ~$150 for a good single sub, $75-100 for a custom ported box, ~$200 for a good amp you're already looking at the same price for the MSBassPro SQ. You can add the MS-WBC wireless bass knob to put up front.
COE6 ~$115 from me
P900.4 $200 shipped from me
MS-62C $200 from me
P662 $150 from me
MSBassPro SQ $450 from me
You're at $1125 for parts for a really nice balanced sounding system that will put a smile on your face every time. Add in your wiring kit of choice for a dual amplifier system(4 gauge) and labor. I'm confident you'd have a better setup than a lot of people.
I would look around, read a lot, learn some and when you actually get whatever car you decide on Then I would look at my options. A lot can change in 6 months. Especially when your young.