I am taking delivery of a 2009 Fusion with Sync and the "audiophile" stereo this coming Monday. During the test drive I was underwhelmed by the stock system, but enamoured with the Sync.
I believe there are some wiring kits that allow interfacing with the stock head unit and retaining it, and using an aftermarket amp. I am unclear on whether or not you could then simply tie in the stock speakers.
I am OK with the general presentation of the sound in the 09, it has only 8 speakers. What I seek it decent bass, but I am unwilling to put a box in the trunk. The stock system has 2 6x9 woofers in the rear deck, and a dedicated amp apparently.
I will be looking for replacement 6x9 woofers (very rare these days it would seem), or 6.5 woofers that can be run IB (no box).