If it is an open concept floor plan, it is very hard to place the rear sides & back speakers where you want them. So what you end up with, is just a 5.1 system for the majority, or 4.1 like some, with all speakers in the ceiling.
Posting a floor plan and pictures of what you have right now, does help in letting you know where you want the sub to place the boxes and plywood for any brackets you may want items placed at (ie flat screen mount, ceiling mounts for speakers if not mounting in the ceiling, etc.). Worse part is, if this is a Tract build, and your hands are tied, and any changes you want, they want to unload your wallet as much as they can, for how you want things.
Now of course the big thing that I would want if I am building a home, is a dedicated closet or space where I have at least two 20 amp circuits for networking and server equipment, a place to wire in a rack for A/V distribution, and network distribution. Then also having boxes up in the ceiling for ceiling mounted Wireless-N Access Points, that are PoE (Power over Ethernet). If you are putting in a flatscreen, and not always going to use the AVRS all the time, I would also want a way to power and place a sound bar with a wireless sub.
Think outside the box, place on a Spreadsheet or legal pad, in two columns: Needs & Wants. Then go through and create another sheet of paper of stuff that can be done later, and what needs to be done now. Also do not forget whole house surge protection, and if you can, at least a way of having remote UPS backup for certain outlets, such as your DVR, HTPC, NAS, along with spec'ing in Surge outlets instead of surge bars at the A/V cabinet, so you get at least a second layer of Surge protection after the Whole house, and you can have the third layer of anything plugged into a surge bar at that point.