Well, I don't completely agree with your rural VS urban assessment, but here are my thoughts on some of your ideas:

2. Outerwall construction - well, start with site selection if possible - in the Northern Temperate zone, a primary Southern hillside exposure is the best, especially if you can add a minor Eastern exposure. Build for your site and climate - there are reasons why the old northern midwest houses are squarish 2 stories with full basements and walk-up attics, for example. A double stud (staggered) wall is better than a deep single stud wall but the difference is only significant in extremely cold climates. I've seen frost rhiming on 2x6 studs in the walls in the winter in the interior of North America - of course, there were other problems (vapor control and ventilation to name two). In most climates bringing the constant temperature line up into the house wall is beneficial, so some version of earth sheltering is worthwhile if one takes the long view (return on investment). Passive solar can have a huge positive or negative effect - it's locale and climate driven. Lots of good books on this stuff (and about as many worthless ones).

3. Roofs and gutters - sure; that's virtually trivial. I'm plumbed up already to be able to do that with a rather significant roof area - but subtly, not blatently so. The part about where to store the diverted water is rather important. I have a short term plan and a medium range plan and the tools and materials on hand to do exactly that. All that stuff is very innocuous and commonplace. For example, dig a hole (you can calculate volume needed very easily) and line it with plastic sheeting. Variations on covering it to reduce evaporation, bird poop, mosquito breeding, etc. You can McGyver the storage and even the collection IF you think ahead a little bit and have a few items on hand.

4. Electrical wiring - nah, no need and it's pretty expensive. Use a transfer switch to cut out the utility service and cut in the generator (or battery-fed inverter) and use your breaker panel to switch off all non-essential branch circuits. All you need to do is take a half hour with a helper to build a GOOD branch circuit map (switch breakers off and see what doesn't have power) and then decide what breakers to turn off. Tape a copy of your list to the inside of your panel and you're set. Don't rely on the mandatory included circuit labels in your panel (what? You mean they forgot to do that! go figure...) - they are not specific enough for this application. You need to know exactly what outlets and lights are controled by which breaker. If you're really into it you can even code cover plates with little color-coordinated dots or something similar... ("green dot breaker controls green dot outlets....")

Caveat: You MUST balance the load between legs on your 220v feed (your genset IS a 220v if it has a 220v outlet, even if you only "use" the 110v outlets) and if you don't know what I'm talking about, get an electrician buddy to help you figure that out or hire that done when you have the transfer switch put in

(BTW, it's illegal to hardwire a generator in without a transfer switch ANYWHERE if you have a connection to the grid because homeowners have killed so many linemen over the years feeding power back out of the house. Also stupid, but that's another debate...)

If you know what you're doing, many jurisdictions allow homeowners to do all this work yourself. If you don't know what you're doing... bite the bullet and hire a pro.

The ONLY reason to run dual electrical circuits would be IF you simply MUST feed some non-standard electrical power (like 12v DC) and don't want the risk of accidentally plugging your fancy 12 volt washing machine into the 110v AC outlet when the line power is on... and in a case like that, your household wiring is too small to carry the required current anyway (can we say "FIRE!") - but those are pretty rare and fancy scenarios. Solid state inverters and voltage boosters are so common and (relatively) cheap nowadays as to make that a pretty desperate move anyway - it's very now easy to condition any input to standard frequency and standard line voltage.

6. Secret closet or cupboard - very good idea; very easy to do in most houses and even rentals (depending on how you do it, it can be "removable" and non-marring in a rental). There have been a few magazine articles about that over the last several years. Think about how much volume you really need and make it no larger - it's harder to discover small hidden storage than a "secret room", which is usually obvious to even a casual observer. You may even find that there are useful hidden spaces intrisic in many built-in features - the fun challenge is in converting them to accessable uses. It's sorta like learning to see varying hares (snowshoe rabbits) in their white camo in the snow - they're invisible until you finally see one the first time and ever thereafter you see them everywhere. Maybe pro burglars develop that knack, too... any LEO's care to comment?

I'm usually interested in this sort of thinking about "what if" - bet there are lots of great ideas floating around here on the topic. Hope my comments are useful to you.

Tom