Morality system as a concept cannot simply be described as good or bad. It all depends on how you use it.
Author made a good example of morality system done badly with Infamous. I like the game, but, true, those choices are pointless. Moreover, unless you stay on one morality path only, you will not be able to access better power-ups for your abilities. Although it is nice to see that if you are a villain people will throw rocks at you.
However, there are games where morality system is at the very least not bad. Mass Effect was mentioned already and I don't think it has a bad morality system, but a limited one. You can basically make Shepard either Lawful Good or Chaotic Good character, but there is no way you can make him/her, for example, Lawful Evil, who uses his/her Spectre status to aid Reapers without commiting actual crimes (just an example).
Although what I said about ME is true about most of the RPG's. They are too limited is the morality choice. Always either simply good or simply bad. What if I wan't to be a lovable bastard, that wants to save the world AND get paid in the process? It's always a choice between Psycho and the Saint. Exception from this rule is Planescape: Torment, but it too suffers from a problem I am about to mention.
All games, in the end, simply make you pick between different paths to the same goal and the only difference between those paths is color of your aura. OK, maybe a few dialogue sequences. I liked how Yahtzeedescribed a balance between good and evil choices: good is safer but slower (meet a girl, take her on the date, blah blah blah) and evil is faster but a lot more dangerous (have sex with a horse and be in danger of geting farmers bullet in your ass).
I think what morality system lacks really is an actual difference between path you take and what are your rewards for your actions. And I do not mean getting "Sword of a Morning Purity" for completing a quest in a good way and "Mace of Painful Penetration" for a bad way.