So, there have been a few hints of innovation in base building games. These are barely even shadows in their games, but they have a lot of potential and shine a lot of light on the basic ideas of base building.
The first detail you need to know when you are designing a base building game is the point. Most base building games have the same basic mechanics, but the game changes dramatically based on the elements that are deepest. Usually, these are the unique constraints that pressure you as you build your base.
For example, in Sim City the supply/radius systems are the deep elements, leading to a game focused on roads, pipes, and pollution. On the other hand, in Evil Genius the focus is on congested space, so the focus is on cramming as much functionality as you can into a limited amount of space while balancing security risks.
Sim City rarely has any concern about security, and there's usually plenty of space. Evil Genius has no interest in supply lines. They have the same basic mechanics, but have different constraints.
Certain games have introduced unusually nuanced techniques. First, let's talk about Fallout 4.
The base building in Fallout 4 is mechanically perfunctory, with little to no complexity or nuance. However, the back end is heavy-hitting, with a combination of modular and freeform components that can be mixed as you see fit. The detail worth considering is hiding in that mess: the power lines.
Things which require power in Fallout 4 mostly need to be wired up directly, so you'll end up stringing physical wires between the generators and everything you need to power. These wires follow some basic rules: the droop realistically as you string them up, and there's a max length, and they can't drag on the ground or pass through walls.
Probably your first instinct was to find this annoying. Hopefully, after a little while you began to see that there is a shadow of something interesting hiding in that idea. Providing power to building interiors is an interesting challenge, involving abusing the droop of the wires to pass them through windows, up stairwells, and so on. The droopy wires interact with the rigid, modular structural elements in a way that is just awkward enough to need careful attention and just flexible enough to allow you to come up with clever ways to do it.
The concept of having multiple kinds of construction that work alongside each other, rubbing elbows awkwardly, is interesting. In the past, you might have to wire up buildings like with SimCity's road, power, and water infrastructure, but the two didn't really clash at all. Later we had the concept of modular structures plus free-placement furniture, but the placement of the furniture didn't really matter much, so it was quite shallow.
This "droopy wiring" system is one that clashes. It means building your structures specifically to allow for wiring, but it doesn't have a simple option to do that. You have to decide the best way to do it, it's a gentle pressure pushing at each design decision. Every time you think you've thought of an optimal solution, you'll see a base someone else built that uses a different technique that seems really neat as well.
Now, the implementation in Fallout 4 is pretty primitive. Space is overcompressed and nobody cares about things like lights and TVs, so there's really no reason to wire things up at all. It also makes no sense that you can't run wires along the walls or floors and have to let them hang.
The underlying idea is interesting. We can use this idea of different construction types butting shoulders freely. We can create interesting new games like this. If we start from the base concept of "modular structural elements", what can we add in that bumps awkwardly against it?
The easiest thing to do is add in multiple kinds of connectivity that have very different requirements and side effects. The basic "modular structure" approach is about creating walking paths - doors, halls, etc. What other kinds of connectivity can you add? Water, power, and air are easy examples.
But you need to make sure their connectivity doesn't follow the same rules as the doors-and-halls structure. They need to rub awkwardly. For example, maybe the wires that can fit through interior walls are limited to only a small voltage, but the heavy cables can't pass through walls and are vulnerable to accidents, fires, and damage from invaders. Maybe the air systems work reasonably straightforwardly in theory, but resonate with the structural chambers to create awful winds and chills, propagate toxins, etc.
Those examples involve integrating into the same construction space as the modular structural elements, slotted into them. However, it can also be in a different construction space, as with Fallout 4. To make this fun, your structural elements have to be permeable in complex ways. For physical objects such as power cables, that means physical holes in the modular elements - windows, doors, or arbitrary gaps. However, you could also have nonphysical things permeate the walls: light, sound, joy, heat, data, whatever. The walls also need to vary to allow those things to break through in different amounts.
An easy way to expand your design space is to focus on things besides power and water. For example, building a "digital base", or a dungeon, or a monastic enclave where natural elements need to flow in order for the monks to achieve enlightenment, or a theme park.
But you don't have to think in terms of connectivity. Another easy thing you can do is think in terms of asynchronous build systems.
For example, instead of power lines, what if it was plants? A fantasy elf village, where you have to grow plants alongside, inside, and as the walls of houses. It would be interesting to try and build your structures to interact with the slowly growing trees you plant. The underground roots intertwine beneath your homes, and the branches crash through poorly-placed roofing to reach for the sky.
Or how about having to build a facility that will wear down over time, and have to build it with the understanding that things will fail and need to be replaced... but have the replacement/repair system take up a different amount of space/resources than the original system.
There are so many other possibilities, and I look forward to thinking about them more.