It’s easy to see what the developers are trying to achieve by including these sorts of choices. If each player has a different experience they’ll have more to talk about to each other, and they’re also more likely to play the game a second or third time to see how it would have panned out had they chosen differently.
You could also be forgiven for thinking that giving the player the opportunity to steer the game at certain times would add depth and meaning to it, but unfortunately the opposite is true.
In the end, it’s difficult to impart a moral choice on the player that is both meaningful and recognisable as a moral choice. In real life, moral choices are complex and often don’t have a polar divide between good and evil, or selfish and selfless for example.
In video games the choices have to be crafted so that both options are viable and reasonable, but distinct, and this is a very difficult thing to do.The result is either unrealistic choices, that are often laughably exaggerated, or similar ones where it’s not evident which is correct.
The latter are more interesting for the player, certainly, but many people feel unfulfilled because they wanted to do the right thing, but didn’t know what is was.
Unfortunately, this is the true nature of moral questions a lot of the time, so perhaps it’s not that moral problems are done badly in games, but more that we don’t want them to be done too well.
All in all it may benefit many games to leave out the moral choice system altogether and focus on the gameplay and core events of the story. Again, which branching plotlines can offer an additional level of depth and intrigue, be wary of them if you ever want to make a sequel as you’ll probably leave a decent chunk of your fan base unsatisfied.