The answers to your questions are based on your preferences. I like a central wiring closet, in a basement or other out-of-the way place. The primary reason is that no matter how neat the installation, lots of wires and terminations aren't attractive (to me).

Cat6 is worth the extra installation cost if you require the extra speed (250 MHz vs. 100 MHz for Cat5e). Yes, Cat6 is more expensive than Cat5e, and usually takes the cabling job out of the domain of the DIYer. I would consider optical connections if you really need more than 100Mhz bandwidth.

My primary recommendation would be to install some form of conduit into which you can place your A/V cables, since no matter which type you install, they're bound to be obsolete in a few years.

kurto has provided you with some very good advice.

As far as your iDevice dedicated system, and not liking in-wall speaker level controls, I don't agree with it.

I don't know if you are single, or have a family, or have company staying with you at times, but unless they all have iPhones/iPads with them at all times, how are they suppose to control each zone that they might be in?

I recommend a traditional setup with in-wall speaker controls, set at mid-range, that then can be controlled remotely, as well as in-room. That then provides individual users to lower sound levels, when needed, without trying to find you or an iPhone/iPad to do it.

So, you have in-wall 16g wiring back to a multizone amplifier (Savant or other brand?), but you haven't really mentioned what you wish to distribute over the CAT5e/6 - RG6 to each location.

Do you also want video in each room? Is the source HDMI/HDCP video, STB distribution, or over-the-top streaming?

Unfortunately, there's no simple solution or standard, so like kurto suggested, put it all in conduit - and I highly recommend with lots of room for new pulls.

"install some form of conduit"

Flexible non-metallic (AKA 'smurf tube' for its sometimes blue color).

if you put it in place from basement (or lowest level) to attic you can then have the option of adding lines and dropping then with minimal wall damage.

Smurf tube is a much better choice than standard PVC since the "rigid" PVC can sometimes resonate in the walls from the speakers in home theater installations. Also, the ridges in the flexible tubing of smurf tube create less friction in cable pulls.

While it may be difficult to find larger diameters, your best bet for A/V installations is 2 inch. The tubing is usually available as blue for electrical, orange for low voltage, red for alarm systems, and yellow for communication systems. As far as I have ever seen, the electrical characteristics are all the same and the color is only for identification purposes. If anyone has seen differently, please correct me.

Anyhow, just remember one thing to prevent one of the biggest mistakes I've seen over-and-over, the molded connector on a standard "type A" HDMI cable does not fit through 3/4" PVC.