In Factorio, you build an automated factory on an alien world whose native inhabitants hate air pollution.
If you spend your time gathering resources manually or with a humble-sized factory, there'd be very little alien hostility. But the better you're playing, the grander the factories, the more you're polluting, the more aggressive the aliens attack you.
Furthermore, trees soak up CO2, so if you preserve them you reduce alien hostility, but if you go fully industrious and build on top of them you invite more alien aggression.
I think this concept is delightful and far from deceptive. It makes the game suitable for players of all levels and it meshes with the game mechanism rather than working behind your back.
hnews folks would also probably enjoy the cellular-automata-like mechanism of the pollution. Essentially the world is divided into cells and each cell has a pollution value. Pollution dissipates to nearby cells on regular intervals. Cells with trees soak up some pollution, cells with machines produce some pollution. A pollution map is available in-game.