I think how New Vegas does it is way better than how Morrowind does it. Morrowind is simply so loosely scripted that the games doesn’t really care if you break it. If you look at Morrowind speedruns there are actually no story beats that you need to hit to finish the game, you can just brute force yourself to the end. But you do have to know how to brute force it because it’s not intended to be finished this way.

In New Vegas Yes Man is a deliberate design decision to let you kill whomever you want and still have the option to finish the story as it’s told. You can do your first playthrough like a maniacal murdering machine, kill everyone in your sights and still finish the game in the intended way. It makes sense from a narrative perspective, it makes sense in a gameplay way (because technically you can kill Yes Man, another one just replaces the one you killed) and it gives you excellent control over the story. You don’t have to go through all the factions to deal with them one way or another, you can just say you don’t care and go straight to the final battle. I think it’s a brilliant solution to quite a few problems that most games outright ignore.