Three weeks ago I purchased a 2010 Fusion Sport with the Sony system (I have driven it about 900 miles during this time). This week I am travelling and rented an SE with the standard radio. I have tuned both to the same Sirius station. My observations are:
The Sony system has cleaner sound which is obviously better but both systems are pretty good. Having said that, neither has the "drive the neighbors crazy bass" that you would get from an aftermarket sub-woofer. Now, I'm 62 (and wish to keep my hearing a bit longer) so I find that at normal listening volumes, the Sony system is as good as any system in any of my friends' Cadillacs, Mercedes, etc. The quietness of the Fusion (both variants) is remarkable for a car of this price-point (which contributes to my appreciation of the sound system).
Also, I was pleasantly surprised at the accelleration of the four cylinder rental car - not like the Sport but surprising adequate in short merging situations. Amazingly, both cars are getting similar mileage in all-around driving. That surprised me. Perhaps it is because you have to push the four cylinder harder to merge into traffic.