Behind the debate was the question of "decorum" or whether or not the work was appropriate to the chapel. The controversy was all the more unusual coming in an age of unprecedented freedom in the area of intellectual and artistic pursuits. There was the nudity thing of course. Michealangelo was no stranger to this debate. It had dogged him all during the time he worked on the ceiling. This time however, he didn't have Jullius II to go to bat for him. As a result, while the bodies remained nude (for all intents and purposes), the genitals were thinly disguised by later artists.
Beyond this though, there was other nit-picking. The figure of Christ was beardless and too young to portray the "majesty" some thought it should exude. The bodies are "heavy" as compared to the "grace" of the ceiling figures. And in the Last Judgement, unlike the ceiling, there was not the loving innocense, the optimism, or the Sunday School lesson qualities that had made his early work so beloved. The Last Judgement is chaotic, hard-edged, frightening, and frankly, to paraphrase Oldsmobile, "Not your father's Michelangelo". In short, the work was disturbing. A cold wind was blowing into the Catholic Church and it's art, and behind it all, was Martin Luther.