YOu can replace the speaker components very easily and continue to use the bose amps. This will have a huge improvement. YOU also can change the head unit but, you will lose the phone connections and will have to redo ALL the wiring. (pretty damn expensive)
I personally have gone with the replace speaker routine. I have replaced the fronts with 6.5 MB quartz Q series speakers and the rears with top line MB quartz speakers as well.
I have replaced the 2 factory subs with 4 8inch JL top of the line free space subs with a Phoenix Gold Zero point Titanium series 4 channel amp to power just the 4 subs. Must say that it sounds 100s of times better.