5. They can be easily manipulated with grinding and exploits (or money)
At the very core, a moral choice system is always a numbers' game. Do something good and you get a fix amount of good points. If you had 60 good points and get 5 more, you have 65 now, which means you became better. If you had 60 evil points and get the same 5 good points, you have 55 evil points now, which means you became less evil. The system is simple, and it works. Also, it's easy to manipulate. By grinding a certain kind of action, you can change between Dalai Lama Mode and Adolf Hitler Mode anytime you want. That's why in games like Fable you can have the whole town hate you for killing some dudes on the street in broad daylight, then love you as a funny guy just minutes later (a phenomenon I like to call The Reverse OJ Simpson) by doing the same fart joke 60 times. In real life, the only thing one could accomplish with that course of action is making everything smell like dead bodies and methane.
I'm sure he wishes it was possible in real life
To make things worse - or better, depending on the point of view - some games even let you skip the whole grinding bit for some real-world cash. Which brings us to...
Dragon Age: Origins. My favorite game from this generation. This game improved on the whole moral choice system by not having any. Your character's alignment is not Good or Evil. Instead, your party members, who all have their own positive and negative traits, opinions and worldview judge you based on your actions. Do something they agree with and they like you more, do something they don't like and they'll disapprove. When you get them to trust and like you, you get to know more about them, they get bonuses (since they have a higher morale fighting alongside a trustworthy guy and not some douchebag) and certain characters can even be romanced (porked). But you have to invest significant effort into getting all of them to like you. Sure, there are some gifts in the game but they don't influence them that much and the more gifts you give someone, the less effective they become. After all, your companions are highly opinionated people. You can't simply buy their affection.
Except you totally can. With real money. Enter the Feasterday Gifts DLC, which contains a number of gifts meant only for breaking the best part of the fucking game. You can get your allies to love or hate you with those things, just to see what happens. You can go from serious disagreements to reverse cowgirl in mere seconds. They are no longer the strong-willed men and women, you don't have to earn their trust and love anymore. They are living bodies with machines inside and you can program them any way you want.
Now, it doesn't take a genius to realize that this pretty much destroys the role playing experience, but unfortunately not everyone gives two fucks. Never forget that most gamers are entitled little shits, and they won't care about fucking up the game for themselves as long as Leliana's panties hit the floor.
"You're a selfish, greedy, immoral person with no respect for the Mak... oh, what a nice gift! How dear of you! Thank you sooo much! Say, you wanna do butt stuff in the tent?"