I second the "anything will sound better", except that I went a step further: components all around. since the grills (in the the doors especially) will muffle the tweeters on a 2-way speaker, so it's best to mount some domes somewhere else. (I put mine in that little space just beside the door defroster vents on the dashboard)
And my personal opinion is that a decent sealed single 10 in the hatch is a fairly perfect match for a "high-power" head unit (read 45x4 or higher). Shouldn't take too huge of an amp to power it sufficiently, and you'll really kick ass without killing your wallet or your alternator. At least you'll actually hear/feel some of the low-end frequencies that a 6.5" just WILL NOT convey. Won't rob too much of your precious cargo space. Some say a powered Bazooka tube will also do the job pretty well.
Also, be careful with the mounting height and depth on those 6.5" speakers for the doors. If the magnet extends too deep, you'll have to remove the factory baffle, and get a custom bracket. If the tweeter on a 2-way speaker protrudes too much out of the top, the grill cover will bubble outwards, and possibly rattle. (This is from experience)
4 good (not great, just good) 6.5" speakers: $100-200
ANY decent 45x4 CD player (go for MP3 if you have a burner): $125-300
QUALITY 10" sub (get a good one...you'll have to replace cheap ones fairly often): $150-200
~250-400 watt amp (for sub): $100