My thoughts upon choices, or why I don't want to join the bad guy

So, one of the main reasons wRPGs are held up as the darling of the industry here and elsewhere is because of the non-linearity they give you. The ability to choose how, when and where you tackle a given situation, whether through diplomacy, stealth, combat, or something else more or less devious than what was previously written here. For some reason, people seem to think that 'being the bad guy' automatically makes a game deeper and better.

A good example of why this really doesn't fit is to look at the Molochean Hand from Arcanum. They're an order of assassins that is dedicated to hunting you and your party down to ensure that the knowledge you possess cannot be used against them. Alright, fine, there's your antagonist. Halfway through the game, however, you infiltrate a camp of the Molochean Hand, and one of the options you have is to walk up to their leader, reveal your identity, and ask for acceptance into the Hand.
Clearly, there are several glaring inconsistencies with asking to join a guild that has been trying to murder you for most of the game.

How do we avoid this, you ask?
Well, the first way is to not give any meaningful choices at all, like, say, in Mass Effect. The dialogue tree is split up into three segments, all of which have the exact same outcome, the only real difference being the words your character says and the colour of the option. This, naturally, limits the game's capacity for non-linearity and generally dumbs the whole affair down.

The second way is to make several bad guys, all of whom aren't really that bad. Examples of this would include The Witcher, where you have to pick between the townsfolk who grew greedy, corrupt and decadent, murdering and stealing from one another, or a witch who used her magic to manipulate the situation to her own profit.

Another example would be Deus Ex, where you're definitely allied against the 'bad guy'(Bob Page), but you have to choose which one of your 'allies' to side with; the former ruler of a secret organisation that wants information control returned to them, the hacker who wants to see the technology that made this nightmare possible destroyed and for humanity to regress, or the AI who wants to rule the world benevolenty and perfectly.

So, one of the main reasons wRPGs are held up as the darling of the industry here and elsewhere is because of the non-linearity they give you. The ability to choose how, when and where you tackle a given situation, whether through diplomacy, stealth, combat, or something else more or less devious than what was previously written here. For some reason, people seem to think that 'being the bad guy' automatically makes a game deeper and better.

A good example of why this really doesn't fit is to look at the Molochean Hand from Arcanum. They're an order of assassins that is dedicated to hunting you and your party down to ensure that the knowledge you possess cannot be used against them. Alright, fine, there's your antagonist. Halfway through the game, however, you infiltrate a camp of the Molochean Hand, and one of the options you have is to walk up to their leader, reveal your identity, and ask for acceptance into the Hand.
Clearly, there are several glaring inconsistencies with asking to join a guild that has been trying to murder you for most of the game.

How do we avoid this, you ask?
Well, the first way is to not give any meaningful choices at all, like, say, in Mass Effect. The dialogue tree is split up into three segments, all of which have the exact same outcome, the only real difference being the words your character says and the colour of the option. This, naturally, limits the game's capacity for non-linearity and generally dumbs the whole affair down.

The second way is to make several bad guys, all of whom aren't really that bad. Examples of this would include The Witcher, where you have to pick between the townsfolk who grew greedy, corrupt and decadent, murdering and stealing from one another, or a witch who used her magic to manipulate the situation to her own profit.

Another example would be Deus Ex, where you're definitely allied against the 'bad guy'(Bob Page), but you have to choose which one of your 'allies' to side with; the former ruler of a secret organisation that wants information control returned to them, the hacker who wants to see the technology that made this nightmare possible destroyed and for humanity to regress, or the AI who wants to rule the world benevolenty and perfectly.

Being good limits the game, but reaps a final big reward. Evil is the opposite but with evil horns and murder.

The best way to avoid the initial problem you mention is to have games with higher quality, that are better written, that don't offer the player ludicrous choices that don't fit with the thrust of the story. Your problem doesn't seem to be with the idea of choosing an evil alignment, but whether this fits with the rest of the game - that's the responsibility of the designers to get right.

Choosing an outright evil path seems to work just fine in Fallout. The GTA games offer a kind of variety of 'levels of evil' choices. We have 30 years of evil alignments in RPGs. I don't think there's a problem.

I think ultimately we're not at a stage where we can truly offer freedom of choice. In my knowledge(admittedly quite limited), the closest any game has come was the original Fallout(s).

The problem with games with a karmic scale is that it forces you to choose what type of character you want to be at the start, then shape that characters actions around that choice.  At that point the amount or significance of the choices on the game don't matter because the game might as well ask you as the start.
"Do you wanna be a good guy?"
YES
NO

I think choices in games are a good thing, but the whole good option/bad option thing should be dropped.  The Witcher did a decent job with the shades of grey approach and I'd like to see that built upon in the future.

How do we avoid this, you ask?
Well, the first way is to not give any meaningful choices at all, like, say, in Mass Effect. The dialogue tree is split up into three segments, all of which have the exact same outcome.

I like the Mass Effect morality system in the sense that it shows you how no matter what, Shepard is fighting for the sake of good, but his methods change based on his personality. That said the morality and its effects are still shallow and hopefully in the sequel there will be more interesting outcomes based on what the player chooses.