Villain Factions in Games to simple ?

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When the villian is too complex and fleshed out, you run the risk of having them be seen as sympathetic and thereby undermine the player's agency to go along with the story and beat them as intended.

I would see this as an opportunity to let the player team up with the villain and have the story diverge onto a completely different path. Maybe the player's side isn't as good as they're led to believe. Maybe there is a greater evil that the villain is trying to defeat and their actions which have been presented as villainous were in fact necessary and can be seen in a new light with the added context. Or it could be something else entirely. Of course, let the player kill the villain anyway and see where that decision takes them if they want to. Replayability stonks would soar to the moon.

but that means complicating the story by usually having to have multiple ending scenarios with the accompanying levels and such.

That would also be the first time AAA corpos would have a valid argument for the $70 price hike. A 'more meat on the bone' kind of reasoning would definitely fly with more people than flimsily excused unfettered greed we've been getting so far but that's a different can of worms unrelated to this thread.