The story and the [intelligence] dialogs mostly. Well, some things in the game just didn't make sense, especially the notion that it's been 200 years since the war, because it definitely didn't look like it. All of the old factions didn't seem right - BOS, Enclave. The fact that, while the world felt pretty dangerous, there was still plenty of PA just laying around and people didn't seem to stick together much - none of the settlements seemed really believable(especially megaton - there is a church, but no trading hub/market???)
I can keep going, but the idea is that once I managed to get all of these annoyances behind me(wasn't easy with the big ones), the game became pretty decent FWIW. Or maybe, quoting Ben Croshaw: "It is the game that finally made me lower my standards and I hope it's ****ing happy"