I agree with you, JPA, that while the iPad with iRule will certainly work, but it's just not good for channel surfing and 95% of your activities. Realistically, the only other question you need to ask yourself is if you will have a server-based media system you want to access frequently without
your video display being on. If your display will be on or you do not plan on a hard-drive based media server, then just go with an RF-based IR system such as the Logitech Harmony remote.
Knowing your situation and budget, plus needed a high "WAF" so your wife can easily control the system, I'd suggest the Logitech Harmony Ultimate. It has RF transmission back to the equipment for IR control. Includes a hub as part of the system to allow for integration of your Smartphone via an app as a secondary control, can natively control Bluetooth devices, such as gaming systems, can control up to 15 different components, which is PLENTY for most systems, and has backlit buttons with a touch screen with macro icons. Setup is also a snap and can be perfectly programmed in under 10 minutes. Here's a link: http://www.logitech.com/en-us/product/harmony-ultimate?crid=60BONUS
: According to Logitech's marketing video, it looks like buying the Harmony Ultimate remote will also get you laid http://www.youtube.com/watch?feature=player_embedded&v=9DxSS4G4Gvg
EDIT: I forgot to mention the Harmony Ultimate will also control Philips Hue light bulbs, which could be interesting for your lighting plan.
SECOND EDIT: Regarding your lighting plan, you have 3 fixtures as screen washers in Zone 1....I'd bump that up to a minimum of 4 or maximum of 5 to get a nice, consistent screen wash - especially with a 14' width screen.Edited by TMcG - 9/17/13 at 1:27am