I have never had a dedicated HT but this is how I would approach it.
I would make sure I get the room itself, wiring, lighting, screen, projector and seating figured out first. If I had to run two cheap old speakers until I could afford what I really wanted I would.
I feel that automated lighting is nice if you can do it on the cheap. It all depends on if you can see to get up and out of the room without it or not.
I would only consider Room isolation if I had kids that used the theater without me in it or if say I had friends over and the wives weren't watching with us. Even saying that it is a luxury that I probably wouldn't pay for unless won the lottery.
I would only do whole house audio if I entertained and wanted multiple rooms to get music with out cranking it up. My wife wants me to do this through just 4 rooms and outside of our home. We have three time a year when we entertain and this could be used.
I like the idea of multiple systems in my home for just me and the wife and our son. Relying on one receiver/prepro would mean it would break. (Murphy's law
)
I would go with multiple subs in room and a Denon 4311 and add an amp later.
I'm just rambling thoughts here... Good luck and have fun with it!