So, separate systems with a single head end.
Make sure you think about how video is getting to your displays. HDBaseT is a replacement for an HDMI cable, so if you have multiple sources you want to feed a single display, then you will either need a decent HDMI switcher in the rack for each source, or you will need separate HDBaseT extenders for each source. I would recommend the former as this will cost a good deal less.
I'm not going to comment on your network. I'm not a networking guy beyond some basics that can get me in trouble.
Not sure if Nest works with C4 still or not. At one point it was, then I heard it wasn't... Nest really is cool, but doesn't play well with others and is really, REALLY stupid in that regard. You may want to talk to your C4 dealer about other thermostats which may be about as cool looking, but play a lot better with C4.
For any surround areas, you have to figure out if you want a local rack to run things, or if you want local sources, and your receiver in the basement. I personally run a rack in the basement and have three local sources in my family room on the first floor. I extend all A/V to the basement using HDBaseT and component video, digital audio, and analog audio for my distribution system. You can certainly run a centralized rack, but it may harm your capability to matrix everything in the future when (not if) HDMI matrix pricing drops.
The key is looking at your drawings and really figuring out where things are going in your home. Where each TV goes, where speakers go, where network and phones will go, then pulling plenty of wiring.
In audio only rooms, I strongly recommend a keypad by each door at the very least. This really allows you to use the system - as you walk into a room you can turn on your audio, when you walk out of the room, you can turn the audio off with one button press.
Video zones can get by with a hard-button handheld remote.
Don't try to get by with an iOS interface exclusively. Handheld remotes are just worlds better and easier to use. The iOS interface is great for complex tasks, but for normal TV viewing, they it just doesn't make sense.
Once you have your list of rooms, zones, etc. make a wiring list. Room by room, location by location. Use the drawings along with the list to ensure that you get all the wires every location they are meant to go.
Finally - Consider ALL the places which are uniquely available and make sense to be wired right now.
My last home was about 2,900 square feet on two levels. We wired for audio in 4 bedrooms, two baths, the family room (surround), kitchen, dining room, living room, study, front porch, back deck, and the garage.
So, 14 zones of audio were pretty easily met in that much space without a problem. My current home is running at over 20 zones of audio.
Unless you are just positive you will 100% never ever even want something, then go ahead and wire for it now. Wiring, in the grand scheme, is really inexpensive overall.