All this talk about rocket stages! Okay, that's done. But let's continue talking about the fundamental gameplay concept behind them: the idea that different functional gameplay elements must be stacked in the same shared space.
This is a great concept, because it's basically Tetris gone off the deep end. When building something, you not only have to build something that functions like you need it to, but you also need to consider the requirements of the next functional piece, providing good anchors and spatial arrangement for that!
Let's consider a classic game idea: you are building a city (or a space base, or a secret lab, or a dungeon, whatever).
Classically, these games operate by building everything in the same basic plane (rarely, with some 3D elements). While you certainly do build the facility in stages as you progress, each of the stages is normally simply attached somewhere in the base. At advanced levels of play there will be a lot of preplanning for optimal final base arrangement, but in general these games can be played "expansively": just staple the next pieces on wherever you can. At very worst, delete a misplaced early piece and then reconfigure a bit.
I'd like to think about how to combine this with the concept of stacking in shared space.
For example, let's say there's a game about a futuristic city. As you build the city, you literally build on top of the existing layer. So your first layer gradually gets covered up as you build a second layer, and so on. However, the lower layers don't vanish: they still operate, albeit in a dark and economically depressed manner.
If you want to build a giant supermall, you'll need to build it right on top of a bunch of tram stations for deliveries (and people too poor to fly space-cars). In order to build tram stations, you need to build them on top of power stations. And so on.
You can make it much more complex. For example, tram stations might cut across several layers, rising and falling to deliver locals to various heights. Landing bays for space-cars might require two layer deep substructures for safety reasons. A giant spire of a building could easily cross a dozen layers. Airflow and weather in the lower layers could be a concern which grows and changes as you stack more layers down on top.
It's a simple enough concept, with a lot of room for whatever complexity you want to add.
We could also go a route with shifting, adaptive layers. For example, let's say this is a game about ghosts coming from dreamers, and you run a sleep clinic specifically to deal with such things.
So you're responsible for arranging all the rooms in the clinic, placing the patients, and creating their daily schedules (including where they can spend their time off and so on). In turn, the dreamscape is manufactured around their bedrooms and their moods created by their day. In the dreamscape you can build another facility to work with the dream-avatars of the patients and protect them from dream-monsters - including those that may emerge from their avatars, or the avatars themselves.
You can stack this N deep, as you like. The treatment in the dream world may involve how they migrate around the dream facility you created, and that may in turn create an "unconsciousscape" or something where you can build another facility to treat all of humankind simultaneously...
Anyway, the key complication to this approach is that the foundations are mutable. If you change where a patient sleeps, or if you introduce a particularly obnoxious thing to their daily lives, the dreamscape foundation will change, and the facility you built there will also be altered - perhaps some buildings lose power, or partially collapse.
Both of these game designs are relatively straightfoward, but they seem like they would be interesting.