general quest design, the factions and reputation systems, real companions, real endings, actual care for the fallout lore and universe, stats and skills and perks retuning, the dlc being godly
i don't think that any of that is debatable and sets fo3 apart from the other ones
other than that i think the writing in fallout 3 is all kinds of terrible (new vegas is inconsistent but has really high highs) and the whole world building thing has been discussed to death but imo new vegas still trumps fo3 in that regard
but those two don't matter so much in the fact that the first things are what separate the fallout series from goofy post apocalyptic elder scrolls
(... And much more, zkylon long post best post, -snip-)