Look at Leviton for your base system (Score 1)

Leviton recently acquired HAI who makes some rather nice automation and security systems (http://www.leviton.com/OA_HTML/SectionDisplay.jsp?section=61367) I would recommend a Leviton structured wiring panel be placed next to your electrical load center, then home run conduit to each room with conduit pull line. Lines for window and door alarm contacts as well as smoke detectors can either be home run (more wires) or in a loop. For your square footage look at the Omni Pro, it handles all of the automation via UPB, Z-Wave, etc and also does security, so you can have all the lights turn on if there is an alarm, or have certain lights turn off/on when you use the fob to arm/disarm. It has an App (snaplink) that you can use for remote control form your smart device. It also does audio etc. I have one of the earlier versions of an Omni Pro (re-branded as aegis) in my house that I got to play with and I use it as my security/fire alarm.