Well, that depends. I haven't played the Mass Effect series yet, so I can't comment specifically on the changes they're making to Mass Effect 3's ending. In general, though, I'll just say that games are iterative, and most areas of a game's design are subject to improvement based on player critique. Obviously, changing a good ending to satisfy the complaints of people who don't understand it is bad; however, by the same token, it's good to change a bad ending when the player base rightly recognizes that it's incoherent and unsatisfying.