A lot of the things that need said about choice in videogames have been said already by reviewers and game analysts alike. However, most of what's being said seems to center around developing moral choice as an opportunity for the player to affect the story and reason out moral grey areas. These have the benefits of making the player feel like they're having a legitimate effect on the universe and allowing interesting and intellectually stimulating moral dilemmas. While this is a great direction for videogame design to take, there is more that can be done with player choice that I feel it isn't being given much attention. I also think that a lot of the common complaints for moral choice are about problems that stem from this challenge.
You see, when someone makes a moral choice it's because they think it's what they want to do. It's almost always even because they think it's the right thing to do. So when a videogame labels moral choices as either good or evil("paragon" and "renegade" are effectively the same) it isn't just painting moral dilemmas in pure black and white with no interesting grey area, it's also refusing the player the option to express and explore their personal opinions of right and wrong. Instead of being like "here is a dilemma that causes you to analyze and reconsider your morals," games tend to instead say "here, find out which one of these two options is right in my personal opinion." I can't count the number of times that even the opportunity for an interesting dilemma was circumvented in the Mass Effect games just because I ultimately knew that I had to choose red or blue at the beginning of the game and stick to it.
This isn't just a rant about why you should actually hate labelled Mass Effect style moral choice systems. It's also the presentation of an opportunity to use moral choice systems in more ways. If you have your game provide the player with an unlabelled grey area moral choice and then side with them whichever they choose, you will encourage the player to analyze, reconsider, reinforce, better understand, or even perhaps change their moral set. This opens up a ton of artistic potential for games.
A great example of game-neutral moral choice comes from a couple members of an older game franchise, specifically MechWarrior 2 Mercenaries and MechWarrior 4 Mercenaries. In these games you choose which of several different factions during conflicts to run missions for. This effects your relationship with all of the factions, eventually forcing you into one of several final missions and endings. These mechanics weren't the best part. The best part was how the game rationalized and supported the player no matter which factions the player sided with. The player's choices aren't labelled as either good or evil, they merely effected the universe and plot. This doesn't just allow for interesting moral grey areas, it makes the player really think about which choice they would make rather than just mindlessly choosing paragon or renegade choices determined at the beginning of the game.