Ya, thorium, uranium, doesn't matter. It is all about reactors in real life. No offence to thorium boosters, but most things on the internet about new technology are basically vast oversells, thorium no different.
Thorium, from a gameplay perspective would be not much different than uranium. Still have a heat source, likely attached to some kind of steam network. Have to manage fuel inventories, have to manage waste (maybe), ect. Uranium/breeder cycle could be used if you want to simulate the most popular (but also least realworld) molten salt, thorium reactor (LFTR). A problem from the realism perspective of a pure thorium breeder is a lack of an ability to have a fissile start load. Thorium has no fissile, naturally occurring isotopes, you would need a uranium235 initial charge, or breeder some thorium->via some kind of neutron bream (hella inefficient). So from a realism perspective, STARTING with a thorium breeder is about the worst idea! And being that it doesn't have much in the way of interesting mechanics over a breeder cycle in uranium, and uranium has a much more realistic starting mode with abilities to bring in advancements later on down the line, I dunno, hard to see thorium figuring in much. Not knocking it, just saying realism wise, no bueno, gameplay wise, not much different than uranium breeder cycle.
Ok, diverting back to some other ideas. I think I have finally come to the conclusion that the idea of "waste storage" is just not needed. Most things in the game reward the player for making a choice to go "deeper" into the tech tree. As such, it seems like the best way to reward a player for going deeper into nuclear tech tree is to treat "waste" as a valuable commodity....something we WANT rather than something we put in a box and shoot with a shotgun. Similar to moving oil via barrels, we want those barrels back!
There are ways to do this with waste as well, either do what the mod I posted on the first page does, and make it part of a fuel cycle that makes fuel and a bit of depleted uranium....not a bad option, but the DU could be removed and not much lost. The factory would need a sulfuric acid and steel, but use less of the sulfuric acid to reward players for recycling and investing, make it the same for how little as the best yield uranium ore would use, maybe even less?! Maybe also have to mix it with some regular fuel as well, but yields back more units than the sum of its parts? Like 1 fuel and 1 spent fuel = 3 fuel...pays to recycle! This quazi-simulates the breeder cycle where you are turning more and more of the uranium238 into usable Pu239. In reality this is usually a losing proposition breeding wise, but hey, it is just a game after all.
This gives us both automation, rewarding complexity without being overly complex itself, and a healthy amount of realism. Once again, the mod on the first page gets most of this right, thought I would want to devs to balance the numbers a bit more.
Also, many uranium ores are, in fact, green whereby many thorium ores are not. So that is totally a plus
Of note, this method produces a bit of pollution via factories, like the sulfuric acid part, the fuel fabrication part, and the resources used to make the plant part. That is all pretty true to life. What we lose in realism, though, is dealing with the fission product waste. I actually think this is "ok" if maybe the factory reprocessing the fuel produces a bit more pollution or something (I guess you could simulate that by making the process longer, right)? I dunno, the idea of managing the nuclear waste sounds like a boring element. Only way I could see it as fun is if we agree that the isotopes in nuclear waste can be used in science (which in a lot of cases they can be) or, after a period of time, turn into blue science, or something like that. Reward the player for hanging onto it and managing it and in a way that is pretty close to reality as many isotopes in spent fuel could be very useful to science (we currently don't really extract them, though).
On that note, you don't actually need a new centrifuge unit, could just be a factory....I just like the idea of a chain of centrifuges....but that might be to complex.
(Edit: Part of me REALLY likes the idea of a factory turning nuclear waste into blue science kind like alien artifacts do. After all, waste is just a resource you aren't smart enough to use, yet. Maybe a couple of advanced science things can make you be able to do this, dunno, what do yall think?)