Rome: Total War did have some weird game mechanics that led to strange ethical problems, though!

Briefly, as a ruler you control a number of provinces, each with a capital city. The taxes you earn from each province are a function of its population size and tax rate. Population growth rate depends on the level of farm buildings constructed, and the tax rate (higher taxes = lower growth rate as some people simply opt out of the cities). "Happiness" also depends on tax rate (lower = happier), as well as level of temple/sanitary buildings constructed. Crucially, happiness also depends on a function of the population size and the number of troops garrisoned in the province. More population = less happiness, but more troops = more happiness (perhaps it makes sense to think of "happiness" as "orderliness"). If happiness falls below a certain level and stays there for two turns, the province will revolt, and other unhappy provinces can join in.

As an aspiring emperor, you need tax revenues. You can achieve this by setting taxes very high, but this makes the population unhappy and lowers population growth. It is better, in the long run, to encourage population growth and maintain happiness through a combination of modest taxation and temple-building. 2% annual population growth soon adds up, and your city with 10,000 residents now has 30,000, which is a nice 3x on the potential tax revenue - more than you could have got by maxing out taxes!

But there's a problem. With maxed-out farms and temples, and low-ish taxes, population growth continues. Soon there are 40,000 citizens, but no ability to build more temples to keep them happy. You can lower taxes, but this just makes things worse, as population growth increases further! Sooner or later, the only way to prevent a revolt is to garrison some troops to keep order.

This runs directly contrary to your military aims: you want those legions on the Rhine or in Persia, not keeping order in some Gaulish backwater. And even if you can spare the troops at first, the number required will only ever increase. Eventually imperial expansion becomes difficult because most of the army is back home keeping the peace. Even worse, you may have to withdraw troops from lightly-populated border regions, making your empire vulnerable to attack.

There is, however, one way out. Provincial rebellions occur when a province is below a critical happiness level for two turns. The rebellion will have its own army, which is guaranteed to be slightly bigger than the local garrison, whatever size that is. The winning move here is to find your least happy province, increase taxes to the maximum level possible, and withdraw the army. Two turns later, rebellion breaks out. You can now move the army back in, easily deal with the small rebel force, and then kill half of the civilian population. This reduces the population to a level where, with plenty of temples and modest taxation, they will remain perfectly happy even with no local garrison. At least, it stays that way for a generation or so, until the population gets back to its previous size and you have to go in and kill half of them.

Needless to say, this is ethically unpleasant! The game gives you no way out of the situation other than mass, organised slaughter of your own citizens. In the later periods of the game, you could convert to Christianity, which gives you more effective temples and allows more populous cities before you have to resort to these methods, but it still only delays the inevitable.

To some extent, this simply demonstrates the harsh reality of imperialism. Having been confronted with these choices and made these decisions myself, I now find it much easier to understand and to believe the accounts of imperial atrocities in history. Not because the game mechanics are strictly accurate, but through the demonstration of how simple incentives can make notionally evil acts seem like inevitable choices that simply have to be made.

I do seem to recall this being somewhat controversial among fans of the game. There were definitely some players who didn't like the idea of running an empire that killed its own people when they became inconvenient. Perhaps they wanted a more sanitised experience! But, as it was, RTW was highly unusual in forcing you to engineer genocides in order to win the game.