Why pure karma doesn't really fit
In Red Dead 2 the honor system worked because the whole story was about Arthur trying to redeem himself. Grand Theft Auto is totally different. It is a satire about being a criminal. A pure good karma system just feels weird in a game where the main point is stealing cars and robbing stores.
But that doesn't mean your choices won't matter. Rockstar has filed some interesting patents that point to a reputation system. Instead of judging your morals it will probably track your notoriety.
How the world reacts to you
Think about it like building your street cred. If your notoriety gets super high because you are constantly on the news for blowing up gas stations, the regular civilians are going to treat you differently. You might walk into a store to buy some snacks and the clerk just hands you the cash register out of pure terror.
It goes both ways too. Some high level contacts on the black market might refuse to sell you heavy weapons if they think you are too reckless and going to draw too much police heat to their operation. You might have to build up respect with different gangs just to drive safely through their turf without getting shot at.
Trust between Jason and Lucia
There is also the Bonnie and Clyde dynamic to think about. The very first poster for the game had the word Trust written across it. I would bet good money that we will see some kind of internal trust system between the two main characters. If you leave Lucia behind during a shootout or take a bigger cut of a heist, that trust level could drop and totally change how they talk to each other in cutscenes.