Morality systems exist to reward consistent roleplaying, but you rarely see them implemented properly.

Let's use the Star Wars universe as an example: Star Wars has a built in reward system for being very "good" or very "bad". The more you stay aligned to your particular side of the force, the more power you achieve. So if you constantly give in to your emotions, you become in tune with the dark side and become more powerful; conversely, if you remain disciplined and disinterested, you become more powerful in the light side.

The negative side of this is that, once you have chosen a side, all your decisions are made for you: you always choose the option that matches your alignment (otherwise you will give up valuable powers).

The problem is that you are never tempted by the other side. There is almost never a reward so tempting that you would consider forsaking your alignment in order to get the reward. Usually the light side choice is always best; the temptations for the dark side are pathetic little bonuses like demanding more money as a reward and getting an extra 500 credits. A real temptation would be the choice between saving the life of a useless stranger and acquiring the most powerful, badass lightsabre in the whole game. The player needs to weigh their beliefs against a temptation that is clearly superior; if a temptation is not obviously a better choice, then it isn't a temptation.

A character who has compromised their principles to gain short term advantages will obviously never attain the highest levels of their discipline - but that same character would have incurred many advantages from being an opportunist who always takes the "best choice". Thus we have 3 states - moral, immoral and amoral. Both moral and immoral characters must invest in their alignment and should be rewarded for their consistency. Amoral characters are always rewarded immediately by their decisions, so they do not gain long-term alignment rewards.

Of course, there is a balance that can be struck - a moral jedi might be tempted once or twice. A moral jedi might give in to anger to gain the strength in order to save the life of an ally. The jedi is rewarded by retaining a party member and friend, but may never achieve the pinnacle of light side powers because he is willing to break from his alignment if the cost is high enough.

It's like the old joke about the beautiful model and the billionaire:

Billionaire: Madame, would you sleep with me for a hundred million dollars?

Model: Yes.

Billionaire: Then would you sleep with me for ten dollars?

Model: What sort of harlot do you think I am?

Billionaire: Madame, we have already established that - now we are simply negotiating a price...

TL;DR - Morality systems fail because they do not provide sufficient temptation to sway players away from their principles.