Well in my short but enjoyable experience of this site, I can honestly say there have been no posts about upgrading the factory audio with aftermarket parts.
Most have simply kept the standard unit or gone for the HK system and accepted its limitations even though it is a good way better than standard. (I have spec'd HK this time myself as I can no longer be bothered with the work required to upgrade - too old now, greying beard and knees that no longer work!)
In the past I have spent some pretty serious cash and built some amazeballs systems in previous cars.
One of the best I ever did was in an E60 BMW.
I kept the head unit, sent all the wires down to a cleansweep amp from Blaupunkt (amp specially built and tuned for the E60 head unit)
This then distributed the sounds around each speaker. I tried the system at first with just a meaty 12" sub in the boot (Focal) but found that the whole system came together better when the little 8" suss under the seats were included, so I replaced them with some Focal units as well.
I can't remember the make of the speakers, I recall the were the latest thing at the time by some Italian company.
Anyway, if you want a sound system on wheels you are certainly looking at the right way of going but I would honestly keep the underseat subs (upgrade of course) use a small but punchy DVC Sub in the boot.
How will you power them? If I recall correctly the system is actually run from the head unit with separate wires going to each speaker thus allowing the head unit to control all frequencies.
My advice would be a cleansweep amp or a cleansweep unit and then an amp.
Anyway, that's just my two penneth worth.
Captain Nerd out