I'm sure there are going to be opinions on both sides of this one. I'm probably not going to upgrade both items at the same time, so which upgrade makes sense to do first. I have the factory CD in the car now.
since you have an 02, the stock deck is pretty un-expandable in terms of amp outputs, and the built-in amp is pretty weak as well. so in your case upgrading the deck or the front speakers will improve things. i know that doesn't really answer your question. if you simply want slightly crisper sound, start with the front speakers-- upgrade to components to take advantage of the stock tweeter location. if you want louder, or more features, start with the deck.
if you had an 04 GT with stock kenwood deck, it would be different. i would definitely start with the speakers in that case.
I'd also go with the deck first. You'll get the benefits of a higher quality amp with more power, and much better EQ features which, from my experience, will typically improve the sound quality more than new speakers would. Then, I'd get the speakers 2nd.
edit -- oh, I guess I don't know what the sound quality is like out of the stock CD player. I was thinking of my stock cassette player, haha.
I agree with the other posters in this thread. Head unit first. The factory head unit sound is really poor.
I replaced the head unit first in my 2002 GT. Next, I added an amp and a bandpass box with a 10" JBL subwoofer I'm still using my front and rear factory speakers after two years without problems.
Other than the lack of deep bass from all speakers and a bit too little treble from the back, the factory speakers sound pretty good. If you wire them correctly and don't overpower them, they should hold up fine. Adding a powered sub or an amp/sub combo really helps.
A good head unit will run 200-400+ dollars; my Sony (with a blue display to match the dash illumination) cost me $240 on clearance. I had the sub and amp from my previous car, so the whole upgrade cost me $300. With the current sound quality, I couldn't justify spending ~$140+ for a good set of component 6-3/4 speakers/tweeters for the front and ~$80-140 for something similar in the rear.