It is going to sound better just because the Pioneers sound awesome. Especially with all the ways the AVIC lets you shape your sound.
I would also take it a step further and replace your front speakers. Go to your local car audio store and listen to some different models. Then use pricegrabber or nextag to find the best price online. And if you do the front speakers, you might as well slap some Dynamat on the doors since you have things taken apart.
Don't worry about your rear speakers unless you want a real project, as they are designed to work with the stock amp and visa-versa. You want your best sound to come from the front anyway.
One more thing. Get the Metra brand dash kit over the Scosche. It fits like it's OEM, except it is plastic instead of metal.