It all depends on money. How much do you want to spend now, how much later? For $250 I could put in 8 all new speakers and a modest head unit that would sound better than the stock system (with a lot of time).
I currently use the factory speakers (with caps to block bass), 2 additional surface mount tweeters ($14) for imaging (I am tall so I sit far away from them) and added a subwoofer. My brother thinks the factory speakers are good enough, but I want to change them anyway to some kind of custom 6 1/2" mid-driver or full range. I also have an aftermarket head unit that I'm not using for power. I just transfered it from an old car since it is a CD changer controller.
I agree with vcontoursvt, the head units will get cheaper or you'll get new features the longer you wait. Speakers are a lot more simple and have limited tradeoffs. However, I don't use many features in my headunit. I just want good, clean power (even though *I'm* not actually using it currently).
Figure out what you want in the end. Sub? If yes, then factory speakers are okay until money allows replacement. No, then you'll have to figure out how much you want to spend on your head unit and speakers.
It doesn't really matter which you replace first. Both will dramatically improve the sound by themselves and once you get the other done.
