The mark of any good villain is their motivation for why they do what they do. Their 'bad guy' label so often rests on their actions, rather than their intent, and while the actions of a character can be misinterpreted, their motivation for doing so is rarely misunderstood.
Presenting the player with reasonable steps that paved the way for a villainous decline tests their own moral compass, which creates an interesting discussion around the justification for the antagonist's actions.
The hero of the story may be shrouded in blissful ignorance to the true motivations of the antagonist, or they may simply disagree with their motivation all together, but inserting an intriguing motivation into the make-up of a villain undoubtedly serves to elevate the overall quality of any video game story, as well as the villain's character. Without Bowser's constant kidnapping of Princess Peach, Mario's heroics are futile, and providing the villain with a great motivation brings legitimacy to why the battle between good and evil exists.
Not every game achieves such a feat. Providing an effective motivation for villainous deeds is tricky, but these ten games manage to get it right.