OK, I know hardwired lighting control is very reliable, but I actually pulled out a perfectly good Lightolier Multiset Pro system from several rooms in our house. While it never failed to work, it was darn near impossible for me to figure out a way to tie it into my automation system, and no one on the boards seemed to have a good answer, either.
So, make sure that whatever lighting system you use will tie in with whatever automation system you select - they don't all play together.
Personally, I've been a HomeSeer user for over two years, and am very happy with it. There were some rough patches when the .net 2.0 version was introduced, but those are long gone and HS Technologies really stuck with their users to get it right. For lighting, I've gone with Insteon and after an incredibly frustrating year, it's pretty well rock solid throughout the house now. I don't know if I'd pick it again, though, if I were doing new construction as I've had a large number of device failures for simple things like the mechanical action of the rocker switch. It's better now, but I'm still replacing switches here and there and their policy toward those who purchase through dealers isn't the best, in my view. It seems many people like UPB, and I've never heard anything bad about its reliability. It would probably top my list if I were doing new construction and were an electrician, as the switches are a bit large and some have reported problems with retrofitting it into standard boxes.
Finally, for HVAC, I'm a HUGE fan of in-floor radiant heat. We installed it in two bathrooms of our old house, and have it in two bathrooms of our more recent purchase. Not having it in the rest of the house is one of the only bad things about the house itself (we bought an existing home rather than building). You just never, ever feel cold with it and it's incredibly efficient. You can even tie it into solar easily if you like. For control, as others have reported, almost any decent automated stat will work. I've been using an X10 one for over two years with basically no problems at all, although for new construction I'd go with hardwire for that.