As people have said, it depends on what you're after. The 6x9's are a compromise speaker - as well all know, very little integrated gear works as well as separate parts.
Me, in your situation, I'd get the 6x9's. I don't have aspirations of entering a car in the next sound off competition, and if I'm in the back seat of a car the beautiful music being heard won't be coming from the stereo
I also don't crank my stereo particularly loudly (though the factory system in my car isn't too bad and can be turned up; for the record it doesn't have 6x9's) so that threshold of when the woofer starts destructively interfering with the other drivers hopefully won't affect me.
It'd "fill" the audio for the scrubs that get relegated to the back of a coupe, and I'd focus on getting nice splits for the front.
Assuming none of the speakers are broken or malfunctioning (I get the feeling from your post that your rears aren't broken), I'd even consider just leaving the stock ones in there and replace factory front speakers instead (as a first purchase). You're far more likely to "hear" an improvement.
In my last car, my original car stereo plan was to replace the good head unit, put in front splits and a (removable) subwoofer, get a nice 4 channel power amp where I could bridge two channels to power the sub and use the other 2 channels on the splits, and then lastly put in rear 6x9's and bridge the amp inside the head unit to power them.
A compromised amp for the compromised speakers. I don't sit back there, and their audio should be OK, so what do I care?