Factorio does a great job of modelling some failure modes of scaling systems.
For example, your train bus smelting depot is fantastic until you suddenly realise you have train throughput issues and need to completely rethink your rail architecture to keep up.
A word of caution, it's called 'cracktorio' for a reason: it scratches a certain kind of itch in a certain kind of brain troublingly well.
For me, the lack of enemies makes the game purely about scale and overcoming "bad luck" with resource allocations on the starting planet and local star system, without having to make hard choices about siphoning off resources to defend against critters
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Speaking of hard choices, I'll also submit Banished ( https://store.steampowered.com/app/242920/Banished/ ) for consideration in the "games that altered the way I think" category. I gained a lot of sympathy for project management after playing that game because it's (mostly?) about prioritizing assignment of people who could be doing any number of jobs, but which of them are the most urgent and advance the goals of the group?
It's actually that "yikes, too close to reality" that makes me not play Banished very often (similar to the Zachtronics games mentioned elsewhere in the comments) but unquestionably I think they're good games and change thinking patterns
For example, your train bus smelting depot is fantastic until you suddenly realise you have train throughput issues and need to completely rethink your rail architecture to keep up.
A word of caution, it's called 'cracktorio' for a reason: it scratches a certain kind of itch in a certain kind of brain troublingly well.