06 Gt stereo help

Start with the deck,yes you can run amps and speakers off the factory deck but it will never sound great.
Alpine heads are still one of the best,probably the cde9846 would work fine or step up to the cda9856 for the extra power.
Kicker 6x8 speakers for the back and 6.5 for the front. Great sound and decent price. KS68 and KS65.
A Kicker ZX300.1 amp running a Kicker CompVR 12" sub in a sealed box. Again great sound,decent price. We sell a ton of the Kicker stuff at work and I personally sold a very simliar system to a girl with an 05 and it sounded awesome!

Now these are just suggestions from my personal experience but the best judge is your own ears. Go out and listen to some stuff in the stores and maybe hit up a car show and ask to listen to some of the guys/gals cars.

I started by replacing the factory speakers in the doors and rear deck. 6x8's fit all around if you want to stay out of the higher (Component) price range. Infinity, Rockford Fosgate, JL, there are so many good sounding speakers for under $100.00 a pair. The next move I made was a new Alpine head unit (9846), some RF 10" subs with enclosure and two RF amps. I also replaced the door subs with RF 8" Stage 1's.

I would start with a new deck. I used my Pioneer with the stock speakers till I got the rest of my system installed. made the sound better. here is the deck I got. i think it looks good in the new dash. Its a pioneer 880prs.

I agree with changing the deck first, but for aesthetic reasons, go with a double-DIN unit
like this one
This one is expensive, but gives a good idea of the size. There are cheaper models to choose from, I just showed the one that I want. I would also go with the amplified Thunderform or the amplified Scoshe enclosure- amplifier and 12" sub in one easy-to-install unit. Change your door speakers, and throw your rear speakers out into the yard. Call it a day.