So I own a 2011 EcoBoost Flex (picture below). I thoroughly enjoy it, aside from a couple little annoying bits. Recently had it in for some brake issues under the extended warranty, and was given a 2016 EcoBoost Flex loaner. I mean, it's semi hard to compare a 2011 with 100K miles and a 2016 with under 4K miles, but I thought I'd share some of my experiences.
My number one issue with my 2011 is the Sync 1 Navi system. As far as I can tell, there is no getting out of it. No upgrades, no retrofits, nothing. It is slow, dimwitted, and has issues "remembering" where you are an audio book. There is no way to skip forward quickly (some audiobook downloads are one big file) so when it crashes, the book starts over, and you are stuck holding the fast forward button for 20 min or more to get back to your original spot (obviously only on the USB or internal HDD). The 2016 Sync 3 was much better, so much smoother and slicker. Easier to read and control. I wished the steering wheel buttons controlled more on the screen, but whatever. The one thing I didn't like was the audio and HVAC controls under the screen. I much preferred the 2011 which had physical buttons and a much cleaner presentation. The 2016 just looked...off.
In my 2011, I really like the analog gauges, they are easy to read and I really enjoy having a physical tachometer. The 2016 forgoes the analog gauges (save for the speedo) for side mounted LCD screens. I have driven and really liked a few cars that have the side LCD's, but I just did not like the layout or the functions of the 2016's. I wish there were more options.
My biggest complaint of the 2016 was the power (or seemingly lack thereof.) The thing I like about my 2011 (which is completely stock) is that 1st gear is a bit of an animal. You get some torque steer and some chirping of the tires. The 2016 just seemed lazy (like they had dialed the torque management especially in 1st gear WAY up). It just felt sluggish. Even my GF, who is not a car person and really doesn't like the "zoom zoom" moments, mentioned how much slower it felt than mine. I don't think the dealer would have the wherewithal or knowledge to throw a tune on, to drastically limit power in lower gears. The whole drivetrain was much smoother and refined, but I liked the rawness of my 2011. The fact I can chirp the wheels into 2nd and the fighting of the steering during launch just adds a bit of excitement and fun. You got none of that with the 2016
After the whole experience, I was dying to get my car back.