While I could come up with some good suggestions, based on what I think you're looking for, here is what I would do. I would list out the different rooms and what I think I want to achieve and then I would probably contact BMXTRIX for a phone/email consultation.
Putting in cat 5e wire is a great first start. As a programmer, I tend to believe that everything should be streamed over a network
Anyhow, I think the idea of controlling everything with a single remote is kind of over promoted. You don't really want to be able to turn off the bedroom system from the living room. If you did that, you would just interrupt your wife in the middle of her tv watching. What you really want is a consistent interface. If you bought the exact same system for each room and then the same universal remote, all you would need to do is leave a remote in each room and know that they behave the same way.
For example, a Sonos system coupled with some external audio amps would satisfy everything you want to do audio-wise (probably) and would be really easy to add onto later on.
For video, HDMI is weird enough without involving switchers and such. Better to just get a good AV receiver per room and run coax for the cable tv feed.
For me, this is a hobby and fun, for BMXTRIX, it's a job so he's who I would talk to if I didn't want to dive deep into this stuff.
good luck!
Jotham
P.S. As long as you take ventilation into acct, contractors can do great things to tuck away A/V equipment so it isn't an eyesore.