It's all about variables. Realistically there's just too much to be going on with. If we imported FO3 into FO4 then there's a headache, many things need to be written at least twice (probably more if multiple things have an effect), but then people would expect to do the same into FO5, creating more variables (everything being written at least four times to account for the variables). The more variables you have the harder it is to work with, to the point that the variables lock the game from being develop-able.
Mass Effect was already slated for decisions not meaning enough. While I love that series and still play it regularly, and even enjoy the continuity through the three games, I have to agree it was a lost opportunity. If a major RPG company can't get it right across three games with a linear story how on earth would a game like Fallout work?
It's just not a realistic expectation. I know in this new world of AAA gaming going mainstream that people expect these companies to work miracles and then they still berate them every chance they get, but these companies are still confined by realistic requirements. Writing doesn't come free or instantly, and every variable accounted for is more time, money, and man-hours. Even Bethesda have their limits.