TL;DR: The new Fable game removes the traditional good and evil morality system, focusing instead on a location-based reputation that changes with each settlement. Players won’t alter their appearance based on deeds but can customize their hero’s look with cosmetics and gear.
I would say its more that morality systems are hard to implement.
If you make simple system where you loose karma from stealing and gain karma from donating money for orphans player can exploit that system easy. You would need to figure some other system. One could be system where after stealing or donating a certain amount you get a status that permanently raises/lowers your karma. But it really cant be permanent either because it takes away from player agency. How would you turn those things to a points. I mean stealing last coin from beggar cant be same that stealing a coin from a millionare. Also this kind of karma system makes so the quests in the game are black and white. You cant make a quest where dooming 12 orphans to die saves thousands from a plague.
How to implement the karma? Everybody magically hating you for low karma is just unrealistic. Should karma effect only some random events and set story points? Sounds fine, but then devs need to implement that system to the storypoints and its not easy to do so without railroading the players. Like Paragon/Renegate in mass effect 2. It made it so everytime the opportunity came to choose from the two, it took away from the real choise and it became just desition to wich stat you want to raise. Also choosing neutral choice was never good option, because in the end game you need to have one or other stat high enough to get trough gated discussions. You could roleplay and choose what ever you feel right, but then some late game options are just locked from you.
I think Elex did it pretty good. Subtil but visible.
Was it any good game? It has been sitting in my library for ever, but i heard its kind of meh, so i have been putting it of.