There are so many details to get 'right' that you could make a career out of it. And what do you know, they're called Custom Installers.
If you want to put in a good deal of time and effort, you will have a decent system, but it will not rival a pro installed system.
Pull the cables to the exact spots, and take a crap ton of pictures, before the drywall goes up. Literally, take hundreds or thousands of pics, to make life easy down the road, when you need to cut the drywall to find that cable. Sort the pics into folders by room.
Drywall over all cables you don't plan to use in the immediate future.
Leave a few feet of cable slack at each end, behind the drywall. Leave lots of cable slack in the wiring closet.
Don't terminate your category cables that you're using (or may be using) for video distribution. Don't use keystone wall plates for those, use wall plate scoop plates aka pass through plates. Keep the number of connectors for those runs as low as possible.
Your in-wall or on-wall tablets/keypads may be powered locally, wired in-wall from a nearby outlet, or may get power from a category cable (or 18/2 cable) run to the tablet location from the wiring closet.
If you don't want to shell out the bucks for full-blown Crestron, find a local Elan or Control4 dealer to make sure you have all the cables you need. At a minimum, run your design by the Elan dealer, to make sure everything is there that he may need in 3 years, when your wife is about to leave you when she can't control the alarm from your iPad app.
If you don't try to do too much - keep it basic, avoid the scope creep - your wife will be happy with it.