I think TitaniumD put it best with his responses.
Just to add a bit...
Auto-wipers: On my car, I just leave them off until it rains, then turn them on. AFAIK, it is common for cars to do that because it makes sure the windshield is clear as part of the calibration so that it will properly detect when it starts to rain, or if it's raining now. I do think it's somewhat normal, but if it bothers you, just turn them off, and turn them back to auto if you are driving in the rain.
Fog lights: Like TitaniumD said, it's perfectly normal on very many cars for them to need to be turned on manually each time you are using the car. The same is true on these cars with the high beams. Fog lights are unnecessary and if you want them on, turn them on. I'm glad they don't come on because all they do is cause additional light in oncoming drivers' eyes, without helping me at all.
Headlights in MFD: Do you have DRLs? I do, here in Canada, and the thing about the Focus is that they seem to have Scandinavian running lights. When my car is on, even with the light switch in the OFF position, my headlights, tail lights, and little orange front corner lights, are all ON. All the time. Volvos are like this too. Every Focus I've seen around here always has them on too. If you don't have DRLs, then maybe this is nothing more than they didn't program a different picture for those who don't have them. This is a global car, and virtually every other place on the planet requires running lights. It isn't a fault, though. Laziness, perhaps.
TIP: Turn your car on. Turn the headlights to the OFF position. Walk around the car. What lights are actually on? Look closely at the front orange and the tail lights.
There are some quirks to this car, but sometimes there are reasons to the things we consider faults or flaws. Many people at Ford in customer service or at the dealers have no idea why the cars do what they do, but some things are working exactly as they should.
As for the dealer experience, that is unfortunate, but nothing compared to what my gf and I have gone through with VW! Major engine/transmission overhauls that they kept messing up and breaking other parts, countless breakdowns as a result, and not a soul at VW cared.
So I can deal with a few things here and there ;)
Good luck with the MFT and transmission issues. Those need to be dealt with and I hope Ford comes around for you. :)