Such a cool idea! After speaking with my gamer husband and thinking about this as a casual level gamer, here are my responses to your questions and tacking on to the discussion above. This is a little bit rambly bc I was writing notes as I was reading. My TL;DR summary: Overall my beefs with video games are that there is no gameplay punishment for exploiting or harming the natural world. I think there would be a lot of benefit in making (environmental) harm reduction and even environmental net benefits a main goal of the story. Management of how much detail you'd like to put into this game will be a challenge.
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Regarding testing regenerative building ideas:
You're talking about resource management games, which I personally like! The earthship is a good idea for restricting the amount of game you'd have to design (initially) to test the concept. It would be very similar to a spaceship in that way. It would make more sense narratively if you couldn't go outside (yet).
This makes me also wonder if there is an opportunity for incorporating environmental costs into your building ideas. These types of games can be very human-centric which is the exact opposite of permaculture/sustainability, where resources are managed thoughtfully to help humans AND the earth. This might be more doable if you're on an island instead of a massive piece of land.
The dependencies of connected systems on the earthship remind me of Satisfactory. See also Valheim. While Satisfactory is effectively a planet exploiting game (part of the overall narrative if people aren't familiar), it would be nice to have planet BENEFITTING mechanisms. The trick for you will be which effects to include to get your point across. My main ones would be: water quality, air quality, soil quality, plant diversity, animal diversity.
The CAD development would be an interesting side effect of the game, but I'm curious if you're reaching for 2 different audiences who want different things out of games. For example, there are players who will build structures to *technically* fit within the rules of the game but they are in no way suitable for real life building. There are other players who would enjoy an optimization problem to build a perfect greenhouse (for example) but these at least in my mind seem to lean more toward people who really like ANSYS simulations for example. One is a more loose gamer looking to progress in the plot and the other is looking for an optimization/building tool.
One danger with having CAD be "usable" is you'd have to somehow incorporate many different pieces of available construction materials into the design. It would get complicated very quickly. For example- glass thickness, plastic thickness, plastic type, wood size and type, metal fittings, R value, actual cost etc. It again depends on your audience (for funsies gamer or simulation-accurate gamer) and the time you have to program these elements together. Managing how much detail you'd like to put into a greenhouse will be a challenge.
I think it is SUPER IMPORTANT to incorporate the environmental cost of building materials into a game like this. Optimization for a nice workable home is one thing, but the environmental cost of these building materials and methods should be incorporated. Carbon footprint, shipping, material quality, longevity, etc. Otherwise for some this might become an exercise in how to build the best greenhouse from materials at Home Depot, which I believe is moving away from sustainability goals.
Regarding the fantasy (game) of an earthship versus the reality (real life build):
Incoporating many different types of used AND new materials into the build would be the most attractive for me. Game example: here is a trash pile with nicer items and some garbage - build the best greenhouse - kind of like the friend slop games that use existing stacked assets. Reusing items will sometimes be more environmentally positive than new items, but they may have unusual non-factory sizes, layers of stuff stuck together, etc. New items may be more useful from a longevity perspective. This is where the "interesting" part for me moves more into fantasy and away from reality. It is more interesting for me to build an Earthship out of trash than it is out of buying new materials. However, this assumes that I don't have to do the labor/keep track of my own energy levels and available time. Another issue that get resolved with fantasy building is cost (do I have infinite money?).
Regarding stacking functions:
Interacting with the outside world (outside the dome) will be a challenge because there is so much nitty gritty with regards to interacting with the environment. One example: how real will the wastewater management work - there are certain effects on plants, insects, and animals that greywater has - how many plants and effects will be included? Making sure that the game is either simplified to include only a few "important" variables will be a challenge. A simple version of this may be: you used the wrong detergent in your washing machine and killed your greywater absorbing plants - use a different detergent/have multiple drainage areas/etc next time. OR you overwatered your plants and have created mold growth in the soil beds and your house - ventilate and dry out your living areas and then clean to remove mold.
Regarding "which challenge to building the first Earthship":
I have 3: Money, energy cost (yourself and others), available supplies.
Based on your discussion above I think it would be worthwhile to make sure you decide what you're focusing on game mechanics-wise. Players having fun may look entirely different than a CAD developer simulation. BUT one may be more popular and reach more people while discussing the same sustainability issues. I wouldd argue that the fun/fantasy one may get the point across without getting bogged down by details. However, if your point is to make people understand the difficulty of building an earthship and making it work, maybe the detail slog is what's needed.
Another idea mentioned by John C Daley was the MANAGEMENT of the project. This should be extended to the before, build stage, and the after of the earthship, as each of these are important.
I think they key to building a game like this is making sure there is a reward structure for the players to help them continue playing. For example, do they rehabilitate a planet? Do they unlock a secret earth manna that helps their game get easier?