The smoke alarm on a standalone circuit is a very clever idea - I wish we'd thought of that!
We also got ceiling fans in the bedrooms - even though we will have ducted air conditioning, ceiling fans use hardly any power and are really nice for sleeping.
You may also want to consider a ducted vacuum - much harder to put in later on. Around $1500.
If you're wall mounting your TV(s), then you may want to consider conduit piping inside the wall to allow for cables to feed through.
I'm pretty sure 2 way switches are extra. From memory, the 'included' electrical plan was very basic - a standard light fitting in each room, and minimal power points.