Hey Scotty I was wondering which would be a better buy a 2016 mazda 6 with the 2.5 skyactiv engine with 60,000 miles for $12,000 or a 2015 Ford Fusion with the 2.0 engine with 90,000 miles for $12,000
Mazda 6 is reliable than the Ford Fusion. You actually noticed that both of these cars have the same price. Mazda 6 doesn't have the cylinder deactivation during 2016 like @daywalker said a long time ago.
Mazda by far, remember to haggle and for sure have a mechanic do a pre-purchase inspection on it.
2015-2017 is the best year range for Mazdas, they had a partnership with Toyota, and its low miles. The Fusion on the other hand, has a horrible EcoBoost engine that has been seen blowing up 4-5 times in just 20k miles of ownership (many instances on this on the forum). I wouldn't pay $6500 for the Fusion. The Mazda is probably worth ~$9000+- depending on where you are.
For longevity, definitely go with the Mazda6.
Definitely get the Mazda 6. Overall the Fusion is a decent car but unfortunately that particular one has the Ecoboost engine.