As for subs... that's much more personal, depending on the kind of bass you're looking for. I like rock bass - very tight and fast, so a smaller sub (10" or a really high quality 8") works for me. Depending on the car, I have one box with a single sub and another with dual subs. In my '11 hatch, I'm using just one, but in my '04 STi, I used the duals because they were in a trunk.
And yes, you have to mess with wires - I consider that the price of admission to better sound. Want it easy? Stay stock with lesser quality sound. As for the steering wheel controls, as previously mentioned, a SWI-JACK + a good HU = working steering wheel controls. As for the AUX port, I didn't bother. My iPod stays connected to my Alpine 24/7 (unless I pull it out to put more music/video on it) and it's living buried in the glove compartment - simpler install and out of the way. Could I have pulled the center console and run a long USB to the back of the radio? Sure. But it was only a foot to the glove box.