Morality systems are fine as a concept, but I've only seen a couple I truly like (Planescape: Torment for one). Most of the time, they're kind of half-assed, and can even be hypocritical; in many games you can steal like a crazed kleptomaniac and still have no morality penalty for it, and in others you can make a decision that (neglecting obscure "please all" solutions that you'd have to be a nutbag to even go looking for) is the best you can make in a situation that is distinctly win-lose, and then get a ton of 'evil' points or whatever.
So, overall, the key problem I have with them is that good and evil are subjective anyway, and in a game characters are often once-removed (at least) from the players actual morality. That, and it is almost always crystal clear what the game considers the "good" and "bad" option. At least in star wars settings, that kinda makes sense with the "light side" and "dark side" of the force. But there is no reward for doing what I as a person would normally do when whiny dipshits try to give me a quest (ignore them) while doing anything else is guaranteed some reward.