I work for a company who installs automation here in Australia (Mox BI VIC). Firstly, the good thing is that you have the opportunity to decide how you want to wire things now if the house isn't built.
1) Start by Wiring back the TPS for lights, downlights, and power points to a single rack. This means that you wont need to crack open the wall to change to a new tech in the future, even if you plan to use a retrofitable system. I cry a little when I see a new house being built, and a retrofitable technology tacked on. Structuring the wiring will make all the difference in the future.
2) Wireless technologies such as Z-Wave are great, however, keep in mind that technologies running on 2.4GHZ need to accept interference. If the idiot neighbors run a baby monitor on those frequencies, and you get dropouts, you cannot sue them, or force them to change. For that reason, only use wireless technologies for retrofits if possible (for multicolored lights, they may need to realistically be wireless though). Do not design a system that will rely on it (except for iPad/iPhone AV control).
3), Run more CAT5/CAT6 than you think you need. And keep in mind, CAT6A theoretically can run up to 10gbit/s up to 37m. There is higher quality unofficial standards such as CAT7A available, however, only install them if you have the money (because, they aren't official, and may not add any real benefit, but are nice to have).
4) Have a 15A socket in the garage. UPS's work better with it, and, in an automated home, it might be nice to have control of some features.. Also, try to get a high-amperage TPS run to the garage (for electric cars potentially in the future).
5) Single story house is TONS less painful for future changes than double. If you are doing double, be doubly sure that the wiring downstairs is right. You might not get a second chance without tearing serious holes in plaster (which we have had to do in a few systems to add/change extra functionality the client later wanted).
6) Run at least 3 Ethernets to every TV. You might want a matrix switch later, and you may also want to control your TV's. If you run a single CAT5 to each TV, you might regret it..
7) You might want electric blinds... Keep that in mind.. You may also want gate lock and front/back door to be openable via intercom.
8) The last problem is wall switches. Unfortunately, many common protocols at this time use a Bus wired system (we use CANBUS, which is utilised in cars also). If you run 6-core security wire in a chain to each point, and RJ45 back to the central rack, you should be covered (albeit, in an expensive way).
9) Pick a standard with an open protocol. To be honest, many protocols can be reverse engineered (it just takes time). If you have the protocol though, even if you pick a standard that dies, it may be possible to develop a software bridge that bridges between 2 protocols, and slowly phase parts of the system out.
Obviously, I am biased, but I recommend MOX Canbus (as I know MOX is committed to the system for the long haul), but, ultimately, the system you choose will also depend on your country anyway (because, it needs to be electrically approved in that country anyway).