You seemed to do most of the analysis yourself. Honda will be more economical. Ford will be more fun. If you want to keep the car for ten years, the Mazda will get you there the cheapest, probably. With a Hybrid, you're going to start having battery aging issues, and so your 47/47 mpg might drop dramatically and require battery replacement.
You mention the Mazda as your non-hybrid option, but the Focus and Accord are also available in very economical non-hybrid options.
Not sure how much of your commute is City/Highway, but even a 20mpg difference in city doesn't add up to much over time. If you drive 10 miles of city every day, 300 days a year, that's 30,000 miles of city. The fuel difference between a hybrid and a non-hybrid, based on some math, around $400 a year. That's not accounting Hybrid battery wear.
I don't really have much evidence to back this claim up, but I don't think there will be much of a cost difference 10 years from now. I think the non-hybrid might be cheaper. Depends on how well you shop and which car you pick.
I think quite a bit of the choice falls on what your commute is like. If it's heavy city with freeway in between, both ways, you'll mulch your battery faster than if it's a freeway cruise.
So, I think you're nearly there. Focus, Accord, Mazda3. Those are probably the best three mid-sizers out there. I'd recommend going out and driving all of them with a good, hearty test drive. Not the standard 'round-the-block special that most dealers will try to get you to do. Drive them, see how you like them.
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