It's not uncommon to hear people say stuff like 'stories were better ten years ago' or something similar, but they often can't put the finger on why they think that. The unreasonable will make up crazy reasons whereas the less crazy try to pick out details that appealed to them personally.
But, I think it goes deeper than that and if we focus on RPGs I have two things to suggest.
1: Voice acting sucks!
I'm not saying game voice acting is doomed to suck from now 'till eternity, but as a general rule it's just not that good for various reasons. Even if the actors are capable they're simply handed a heavy binder full of words to be read into a microphone. As long as that tasks is completely things like characterization, shifts in emotion depending on the situation and that unshakable feeling that they're not talking to you so much as reading a list to you aren't important enough to get right.
In games like Torment and the Baldur's Gates there was very little acting. Most characterization was done through text where shifts in mood and expression were described for you to imagine rather than implied and not really followed up on by the actor/character model. Basically, we remember the stories and characters as better because we were left to, for the most part, imagine them rather than have a bland performance forced upon us.
Still, I think the craziest part is the gamers of today who claim to love the acting in games like Dragon Age and Mass Effect, standards fallen so low that they would be blown away by some random soap opera on tv. The procedures for voice acting need to improve a lot before they can compete with our imaginations.
2: The main character could be smart.
In the more recent BioWare games I get the feeling the people who claimed Inception could never be successful because of its complexity have a hand in the game of modern video games. Most responses in BioWare's more recent titles results in the NPC calling you a moron and disproving sort of brushing the protagonist like a dumb child. And often that's what the dialog feels like. Even the 'power'-responses that you gain through influence or good/evil-levels seem flimsy and of no higher consideration than any other words one could've chosen. But the jesus-touch of the protagonist makes even the most ineffectual argument seems Ciceronian if backed up by enough paragon points. It heals the addicts, it stops the ruthless murderers hand, it scares the fearless warrior races.
Of course there are plenty of examples of this in earlier works from various companies, but there's one thing that's slightly different. As long as there were intelligence and/or wisdom stats there was room for longer, more convincing arguments, not seldom something that extended past one exchange. The extended conversation you have with Dak'kon in Planescape Torment is a pretty good example of this, were you actually start shattering a man's perception of reality. It's not quick, it's not badly underbuilt and it's not something that has immediate effect on the character.
All in all, I think it's time to do something with the 'intelligence'-tool again, because playing as a idiot space marine or medival moron isn't really that flattering since it suggests the player isn't smart enough to figure things out past what you can put into the character's mouth. If you're constantly several steps ahead so to speak it just feels frustrating, and you can't adapt by for instance maxing out the intelligence stat
edit: As for Alpha Protocol, your choices can change the story monumentally. What is this dude talking about?