With products like the JBL MS-8 and the new Rockford Fosgate 3SIXTY.3 (not released yet) there is no reason IMO to replace complex factory head units anymore. Personally I would go with the MFT setup or factory radio with sync if you want a lower trim model and using these devices to do all the sound processing. These are HIGHLY complex devices that not only allow you to retain a factory look (less theft!) but also drastically improves the sound overall in the vehicle. You could keep everything factory on say a Focus SE with sync and install a JBL MS-8 and you would notice a SIGNIFICANT improvement in sound since it has an onboard 8ch amp AND flattens the terrible Ford factory eq and will even auto eq the car for you (home theater technology)
I have been in the mobile electronics world now for 8 years now and most aftermarket head units are being stripped of their nicer eq settings and or crossover adjustments in lieu of connectivity. Alpine and Pioneer have seen a sharp decline in overall quality over the past 4 years. They are still good radios but not like they were in 04 or 05.
With all the new vehicles coming out and how the audio system is integrated with everything else in the vehicle you are going to start seeing OEM integration is the future. I have been preaching this for years now. Granted some of the new dash kits have gotten a lot nicer but costs have sky rocketed. Recently I installed a new double din head unit in a 2011 Camaro and the dash kit/harness combo was over 300 dollars.
2009 SES Coupe #036
MECP Certified Installer