I was thinking about this the other day, i would love it if there was a game where, for the first half you played as the stereotypical 'good guys' and the enemies were presented as the stereotypical 'bad guys', but for the second half you saw the game from the enemies perspective, and had to play as them, perhaps at the end you would have to choose a side to win?
Anyway, i agree, video game villains very rarely have any motive other than 'because they're the baddies', and i'd love to see more games which challenge the typical perception of 'good' and 'evil'.