First off, the reason those games doesn't have that many options is that the more advanced our game engines get, the harder they are to work with. While they sure look nicer, and work smoother, for the user, they are hell to work with. It used to be all it took to get a character in game was a couple of dialogue lines and some code. Now you need a customized, fully animated model, a voice actor, behaviour scripting and god knows what else.
For an action to have consequences it's the same, if not even worse. Giving the player choice and have the world react to everything is going to be hell. Since it's time consuming, and can easily be hidden from players, at least on their first playthrough, many developers skip it.
Anyway, on to the real topic. I disagree with you that it's bad to use good and evil in a game. A game will never truly work, and has to abstract some things, this among it. Being fiction, good and evil do exist in many games. Star wars and the dark side for example, or Sauron and his orcs. They are truly evil.
Even in other games, like Fallout or similar it is a viable abstraction, even if it can of course, be done variously well.
The problem as I see it isn't that you're either evil, or you're good. It's how it is portrayed. In games you aren't evil for a reason. You're evil because you're evil, you're evil to be evil. There's very seldom any real motivation to it.
The same thing goes for if you're good. Being good means giving away money, and doing quests. End of story.
What I think is the solution is not to remove good and evil, or a karma meter, sure, that might be the best for some games, like Heavy rain, but it most games it works. The solution is to have the choices make sense, have them be sensible. You can probably see that giving money to a beggar when you're walking down the road is an act of good, and what is "right" to do. You might still decide to keep the money, you might need it for something yourself, you might think someone else needs it more. In the same instance you can probably tell that some of the things you do irl, is also "evil", or at least some of the things you could decide to do. That might not stop you from commiting those deeds, if you had a reason.
Since in a game the only reason to commit an evil act is often THAT it's evil, the moral dilemma is out. In the second Fallout game you really had an oppurtunity like that. Really early in the game you could become a slaver. Sure, it's not very nice to do, and it carried some severe consequences, but the pay was good. I mean REALLY good. That early in the game, it was heaven. No more struggling to survive every encounter, no more being afraid of what might pop up behind the next corner... You could afford weapons, and armour, and ammo. You could afford medpacs and stim packs. It truly was a tempting offer. Sure, it was evil, but so what?
That's how it should be. You shouldn't have to try, and try real hard, to be evil. Look at KotoR for example, where the only way to be evil, is to not only rob people, and kill people, you have to dig up their corpses and rape them in public. Your companions still won't bat an eyelid though. They might complain that you use the force to do it, but that's it.
I agree though, that a game should not try to teach you a lesson about being good. If anything the journey should be enough, and make your slowly realise how awful you're actually being, or what consequences your actions have. It should be someone scolding you because you acted evil in the game, you should get what you were working for the whole game, you should get it all, and it should bloody hurt.
This worked really well in Neverend according to me, if you were evil, it was mostly because of who you allied with, and how you proceded to do things. You could choose between expelling a demon and making it your slave, for example. You could choose to react in horror when another character was thrown into another dimension, or you could be amazed at the spell used. If you completed the game as an evil character, you got through. You summoned an army of demons, and you became a queen of the whole land. You looked bloody badass doing it too, and while I cackled evily as I watched the cutscene, I still couldn't help but feel for the people in the town my demons massacred. They were pretty nice after all.
That's how it should be done. If there is a morality lesson in the game it should be taught by example, it shouldn't be a lecture. Here I truly agree with you.