3. The Games Reward You For Being Pure Good Or Pure Evil (Thereby Punishing You If You're Anything Else)
Developers really like their extremities, don't they? Not only do they give options in absolutes (and don't forget, only a Sith deals in absolutes), but they almost always give away some sweet special power or bonus attributes if you pick one side at the beginning of the game and then go all the way on that side. A good example is the Karmic Overload in InFamous. That basically takes out the role-playing aspect and the decision-making part of the decision-making gameplay mechanic, reducing it to a simple question of ?Which side are you on?". That is, as long as you want to maximalize the power of your character, but who wouldn't want that anyway?
Ready to unleash electric Armageddon with the power of kindness
This can be defended, of course. It's not like your character will lose some of their power if they don't max out the Good or Evil spectrum. It's just a little reward for those who go beyond the call of duty, becoming the reborn Jesus Christ or Satan himself, respectively. But the point is: by rewarding them for doing the same Good/Evil options over and over again instead of thinking for themselves, they punish everyone else. Making my own decisions is awesome and all, but when I think about the +3 Dexterity my Sith Assassin could get for free if only I killed everyone the game lets me kill (even those I don't want to), and were mean to everyone in my group (even to those I really like) then my sense of justice and fair play overrules my judgement. I MUST get that free bonus at all costs because others got it, and I don't like being left out. And forcing me into this dilemma every time I play Knights of The Old Republic II: The Sith Lords gets Obsidian a shitload of Dark Side Points in my book. Speaking of sequels...
4. Sequels reveal your decisions have little to no consequence
The great premise of games with a moral choice system is that you can influence the world around you. You have a say in who gets to live, who dies, and in some extreme cases you can even decide the fates of entire cities, or even planets. Then the sequel comes out and you realize your choices amounted to jack shit.
Going back to KoTOR again, if you were a righteous Jedi Knight, you defeated Malak, destroyed the Star Forge, and led the Republic and the Jedi Order to victory. But soon you left known space in search of an insidious threat, and without your leadership, a new bunch of Sith hunted down and killed the Jedi. If you were an Evil Sith Lord, you defeated Malak, used the Star Forge to destroy the Jedi and much of the Republic Fleet. But soon you left known space in search of an insidious threat, and without your leadership your fellow Sith turned on and killed each other, allowing a new bunch of Sith to emerge. So... what changed based on your actions? Absolutely nothing. In both cases, both the Jedi and Sith Orders from the last game are wiped out, the Republic is still weak due to the heavy losses they suffered in the previous game, Revan is nowhere to be found, and The Sith Triumvirate seeks to destroy the last of the Jedi.
"So... what the fuck did I accomplish?"
I understand why they chose to make the story like this. There are so many differences between the Good and Evil options in these games that they might as well make two sequels, a ?You were a Good Guy Edition" and a ?You were a Dick Edition". Obviously, that would increase costs, development time, and it's a pretty safe bet that most gamers wouldn't buy two separate versions of the same game just for that.
Or would they?
On the other hand, despite being a festering pile of poo, Dragon Age II solved this problem in a surprisingly elegant way. By having the sequel take place in a completely different location and the main plot having next to nothing to do with that of its predecessor, it doesn't come across as cheap when things largely happen the same way no matter what you did in Origins. Only the side quests change, but they change in a somewhat significant way. It's not perfect, mind you (Leliana is alive despite the possibility to kill her in Origins), but it's a step in the right direction.