Read this thread for the best MPG info on the net:
3.73 gears, if you're going to ever tow, or if you're going to want to crawl increase tire size a little (not a lot) is going to be better. Your mileage will suffer a bit, but not much - if you read the thread, you'll see that it's more about driving habits and conditions. 3.73 from the factory is $50 difference. Changing gear ratios later is significantly more.
I have a JKU sport S manual with the 3.73 gears, and I'm usually right around 20mpg, and at highway speeds (60-70) am typically running at the bottom of the 2K rpm range. I don't drive in a hurry in my Jeep, though.
The 2dr and the 4dr both have advantages. Unless you're buying it just to offroad with, the 4dr will have benefits you'll notice quite often.