I love this post. I changed the 4 door speakers for Kickers from JB HiFi, about $320 total. Splits in the front and duals in the back, and I took the centre speaker out and the sound was a lot less muddy after the upgrade.
To anyone who has done the speakers and not the rear parcel shelf, WOW what a difference!! It is worth the 2-3 hours it will take. (mostly to remove the seats and shelf then re-install - dynamatting took 1/2 hour)
I left the original subs, but like most people found, I swapped the speaker wires on both. Then I got some dynamat from Jaycar, and covered the rear shelf as much as I could (press it down hard!) - there are locating holes, screws and wires to go around, but holy crap the bass difference is amazing! Dont bother changing the rear subs unless you are going to rip them out and put a box and amp in the boot. But, I had a box with dual 12" carbon fibres for years in my last car, sounded frighteningly loud but now I prefer the extra space i have instead, especially after this mod!!
Now i'm not so fussed I only have the stock system.