I have the base radio too. I have installed 5x7 in the doors and rear deck. It sound a little better. As far as what type/brand, its your call. I'm keeping the head unit, due to so so review of the kit made by Mitra. Hopefully in a few months other radio kit options will be available. My next step to to add an amplifer. I did noticed the sub enclosures are attched to the door panels. I was thinking of installing 6.5 compoment speakers, by cutting into the panel. That will wait after the amp install.
There's no need to cut into the panel. You can just make an adapter to go from an 8" down to a 6.5". The easiest way to upgrade those is to just get the Kicker/Shelby door subs. Then if you're going with an external amp, personally, I'd love to get the Image Dynamics 5x7's that fit right in the stock location but sound awesome. I'm not sure if I'm getting an external amp, though. I'm not quite sure if I'm ready to tear the interior out of a brand new car.