Sounds like an exciting project!
Definitely 3 wire, as it will give you many more choices in devices, both now and in the future.
And definitely keep some physical wall switches, in fact you may be required to do so by local safety codes. You do want to make sure that if emergency services has to come to the house there are ways to turn the lights on in the extension even if the home automation system is not working or emergency responders are unfamiliar with it.
@anon36505037 is in the UK and Has now done Two full houses with zwave kit, one retrofit and one new build, and should have lots of advice for you. 
You can start by looking at his most recent project here (the topic title is a clickable link)
https://community.smartthings.com/t/new-house-build-update-uk/131433/