I've gotta say, I'm actually really surprised that there are this many people who are glad that they got rid of it. Like I said before, I can go either way on it so I voted 'don't care'.
Exactly. I don't want a game to decide for me what is right or wrong. I'm strongly of the opinion that the Institute is the evil faction in Fallout 4, but other people see it differently, which is fine. There's a good argument on both sides of the debate, and the fact that there is no clear cut answer to this question makes it a lot better. If there was Karma, we could point at it and say "See, when you destroy the Institute you gain/lose x amount of Karma, so obviously _________ing them was the right choice."
I don't want that to be decided for me.
In Fallout 3 you could activate Project Purity and gain a ton of Karma. Or you could put the modified FEV in it and lose a ton of Karma. Personally, I happen to agree with this. However, that doesn't mean that there isn't at least some kind of 'greater good' argument to be made for adding the modified FEV. There are plenty of arguments to be made here. But the game made it clear that Project Purity=Good and Modified FEV=Bad. It was decided for us ahead of time that one of these was the good choice and the other was the evil choice. That takes a huge element of role playing out of the game for me.
Many people like to think that there is some universally objective sense of morality, but I've never been convinced that there is. I think in some cases there can much more of a clear cut right or wrong answer, but in most cases there's a lot more of a grey area than anything else. My sense of morality may not line up with another persons. Abortion is a good example of this. Two people can be on opposite sides of the debate, and both will be absolutely convinced that they're right and that they're taking the moral high ground. Is one of them definitely right? Well, in my opinion, yes. One of them is absolutely right. But other people may think that the other is the one who is absolutely right. Morality is a very subjective issue, despite so many people holding a view that there really is some objective sense of morality.
What the Karma system adds to the game is basically an objective sense of morality. Doing x is absolutely the -good- thing to do because it awarded positive Karma. Doing y is absolutely the -evil- thing to do because it awarded negative Karma. It's hand holding. It's a reassurance that you're doing the good thing, or reassurance that you're doing the evil thing if you're playing an evil character. I don't need the game to tell me if what I've done is good or bad. I should be able to answer that question myself based on the choices I've made and why I made them.