Ive had 7 or 8 cars now all with decent sound systems in, and people who are saying how important good wiring is are spot on, it can make a huge difference.
As for brands, in my own experience, Kenwood are probably the worst ive come across in all aspects, but my alpine amp is top class, all be it I paid 400 quid for it! If you're looking for a cheap HU, value for money I found Clarion to be the best, and anytime im not shelling out 100's on HU's I always stick with them.
Also, as somebody previously said, save yourself a few quid and sack off 6*9's, most normal car speaks are more then adequate once amp'd, and everything gets to stay original and neat