It devalued all the side-quests I took on before, and made them pretty insignificant to the whole story. Sure, in the short run, I saved Big Town and taught them how to use guns, I defused the bomb in Megaton, I liberated Harkness and killed off Zimmer and his bodyguard for him, I released Harold from his torment (NOO HAROLD HOW DID BETHESDA SCREW UP YOUR CHARACTER D

, I stopped the two crazy people from making a mess in Canterbury Commons, I helped write the Wasteland Survival Guide perfectly, I yaddayaddagoodkarmayaddaetcetc. But when all I saw was just that I gave clean water in the Wasteland, and didn't tell me what happened in the future, it took away the whole point of doing the sidequests. I honestly thought that it would be there in the ending, telling me how awesome I am, much like the previous games.
Also, the whole Jesus Reincarnation annoyed me to no end.