Yeah, I fucking detest the way morality systems in games work.
I don't think they're a fundamentally unworkable idea, but very few games have even come close to doing anything good with the concept.
Most just offer you two equal but different benefits, let you pick between them, and call that morality. See Bioshock. And the Mass Effect / KOTOR system always sucked because it punished you for going down the middle (ie, playing a complex character).
One of the only good morality systems I've ever seen is Metro 2033. For those who don't know, the game has a secret personality tracker. It gives you points for taking actions that are pro-social. You get a lot of opportunities in the game to refuse benefits or give up resources to help others. You are never directly rewarded for this. It doesn't do the bullshit where you give someone some food and they go "Here's an old gun I had lying around." Being kind costs you. It also measures the time you spend interacting with people, listening in on conversations, that kind of thing. Just generally giving a shit about other people. By the end of the game, if you've played your character like someone who cares about other people, you get an opportunity to make a better choice in a specific situation, that leads to a better outcome. If you don't, the choice is never presented to you at all, because the character you portrayed wouldn't even think there was a choice to be made in that situation. It's brilliant, and it completely solves the usual Deus Ex / Mass Effect "Three buttons" ending where nothing leading up to it matters. To be able to make the good ending choice you have to have played the kind of character who would be willing to make that choice in the first place.
Neither of these axes are either/or propositions.