In my opinion, theres nothing wrong with having 6x9s and a sub. A mate of mine used to have 6x9s and a sub, but then removed the 6x9s cuz of all this rubbish that everybody was spouting. Now, he has front components runnig off an amp with just a sub and an amp in the back. Hes running the standard speakers off the head unit for "rear fill". However, it doesnt sound anywhere near as good as what it used to! Whenever you turn your head to look left then right at a junction, you can hear a massive "hole" where theres just something missing! Also, when sat in the back of the car it sounds terrible as there is way too much bass and not enough treble and mid. The sub over powers everything!
Ideally, he could do with some bigger speakers fitted in the rear door cards to aid the "rear fill", but to be honest, he shouldve left the 6x9s alone!