The problem as I see it is that I doubt video game morality systems can ever be anything but consequentialist, yet attempt to force an illusion of deontological ethics and objective morality onto the player. When a player sits down with a game that has multiple morality "paths", they've made a decision prior to playing about how they're going to play and all else is pursuant to that final cause. Moral choices in the game are not made in and for themselves, which is what the game would have the player believe, but for what consequences it will have.
This problem is compounded when game designers craft labels, which add a sense of objectivity to the game world being crafted. If a Shepard is paragon or renegade in Mass Effect, they are such because the designers have deemed a particular course of actions such. When incentives, alternate character growth methods, or plot paths for adhering to a particular moral path, and make deviating from that or playing in alternate ways detrimental (as, again, is the case in ME1/2), designers encourage or outright force players to adhere to the morality they've enforced upon the game.
That, by the way, is the reason KoTOR2 is one of my favorite games of all times when it comes to morality systems. Chris Avellone deconstructed the hell out of Star Wars' innate morality system, illustrating the would-be deontology of the Jedi is far more nefarious than advertised while showing the Sith to be far more deontological than expected, and I loved every second of it. Add in the fact Kreia is a notoriously unreliable narrator, known pathological liar and manipulator, yet pushes the character to elect morally-grey choices which forsake morality-based incentives, and you end up with a fourth-wall shattering deathblow to the light side/dark side mechanic.
The only solution as I see it is to chuck the whole idea out as holding game morality back. Throw out the illusion of deontology, get rid of incentives tying the player to a designer-enforced path, and let the player make up their minds for themselves whether their character is doing the "right" or the "wrong" thing, and whether their characters are good or evil. Dragon Age and New Vegas did a pretty good job of that while maintaining some vestiges, and they were dramatically better off for it. Let's get some postmodernism up in this bizzatch.