I can think of some obvious examples to start with, but my subtle but insidious nominee is Fable III. Fittingly for a pretentious grifter like Molyneux, the game requires you to raise a specific amount of gold or your kingdom is destroyed and you get a bad ending. The goalposts are moved by the game if you raise money in ways it doesn't approve of, and it is simply impossible to reach the fundraising goal in any way that isn't at least Enlightened Centrist levels of evil, the kind that lanyard-wearing neoliberals giggle about. That's right, you need to be at least this evil or your kingdom is destroyed. So deep and really makes you think about the hard decisions that are made by the ruling class, doesn't it? :zizek:
Nah, it's intentional. Elder Scrolls games generally don't have "good guys". Both the Empire and the Stormcloaks are intended to be understood as, at best, deeply flawed. If the Empire wins home rule gets crushed and Skyrim is violently reintegrated in to the Empire. If the Stormcloaks win the Empire is badly weakened, leaving it in an even more precarious state and unable to effectively resist the Aldmeri Dominion. And the Aldmeri dominion wants to unmake reality for religious and ideological reasons.
This theme goes back to Morrowind, where the Empire openly does Imperialism, but the traditional Dunmer houses are slavers.
Also, the Empire is trying to placate the Fascist Aldmeri Dominion, but Ulfric is an Aldmeri tool. The Dominion arranged for his escape behind the scenes so he could destabilize the Empire. They set themselves up to win either way.