Lots of people install a new head unit, bypass the factory amp, replace the 4 door speakers, ignore their rotted out sub and are quite happy.
I'm unhappy with my setup (all aftermarket, no sub) because the storage system I put in place of the second row covers up the rear door speakers and pretty much leaves me with the front doors only. Maybe the headliner speakers, too...I've never checked. But I don't care enough to do anything about it. Sound quality from an iPod sucks anyway. As does most music (have I ever said that before???). Besides, my $20 Baofeng gets FM and the center console makes a nice natural amplifier for it!