The ending slides make you feel like garbage if you help a single faction leader, especially with Caesar and House. The best ending, with the most people ending up in a good situation, revolves around rejecting each faction and taking over the middle one.
At worst, there’s minor mechanical dissonance between narrative and design, but it’s nowhere near the level of the utter shit show that is the entirety of Bioware’s TOR MMO.
This is mainly because karma isn’t a morality score, it’s a faction popularity score. The what goes around comes around nature of the system is less based on being good or bad and more on how much a given faction is likely to help or hurt you because of how you’ve interacted with them. Thus, karma is based on the given uniting philosophy of that faction, but it doesn’t represent the morality or philosophy of your player character. Do a thing the faction agrees with that helps them, gain karma, and you lose it if you do the opposite.
I think if the karma term was dropped, the system would make a lot more sense. The same can be said for the Shadowrun games, which reward karma for impressive feats and less for any sort of moral action.