Hey its alright, I have encountered similar issues with a proprietary game engine just not being nice about savedata handling or dealing with large multidimensional arrays, though unity really should be able to handle all that data, is it all stored in map tile objects or something like that? That might be it, try storing the map separately from agents and nobles and stuff, like maybe its expecting to write a block of data each iteration of the writing loop that is much less complex, IDK. I know of unity games that supposedly handle equal, if not larger and denser amounts of data.
If all fails, then I can recommend Godot, much better licensing(you don't have to pay a single dime no matter how much you make, you can release your games and software with any license you want, you fully own the product of your own design and labor), skills carry over just fine from Unitys SDK to Godots SDK. You got full access to source engine code, too. Engine is written in C++ and it supports both C# and their own (very trivial to learn) python or JS like language for scripting, and the community is really, really helpful and supportive.
Regardless, I wish you the best of luck in making this game, I love playing it!