I like manuals and have had one in every vehicle I've owned since 1985, but they have their downsides. They suck if you drive in traffic a lot and, believe it or not, if you ever have a transmission problem, they're actually harder to work on and will most likely cost you more than an auto trans repair. I was the "tranny guy" at a local Dodge dealership and we shucked through automatic transmissions like they were nothing but always hated seeing a manual come in. Doesn't seem to make sense, but it's true. Automatics are easier to work on. We just worked on a lot of autos because they far outnumber manuals.
If you're concerned about mileage, I would imagine a lot of that disparity between mileage with an auto vs. a manual transmission could be negated by driving habits. It's easy to mash on the gas and accelerate fast away from a stoplight in a car with an automatic transmission; not so much so with a manual. I think a lot of people decrease their mileage with an auto trans by thinking they're John Force when the light turns green.
I suppose the auto transmission requires more energy from the engine to operate, drag, etc. but if you "drive it like an old man" most of the time, I think you'd see that gas mileage gap get a lot closer to the manual.
Oh, and in case I didn't mention it, sticks suck in heavy traffic. It's personal preference, of course, but after 26 years of driving a stick, my next vehicle's going to have an automatic.
In my humble opinion, you made a great choice. Everybody seems to think the Focus is a great little car.