Perhaps the fact that two of your films were either directly or indirectly about Christ is most likely why Last Temptation of Christ isn't on your list. Then again, maybe you don't think this is Scorcese's best work, even though it was one of only three films in the 20th Century that he got a Best Director (and if that's not controversial I don't know what is)
I'm honestly not sure whether the world was more or less up and arms over Scorcese's adaptation. What I'll say is that when Roger Ebert was invited to a solo screening of the film (which he would one day put on his list of Greatest Films ever made) he was warned not to tell anybody under fear that it might end up with harm coming to him.
He views as a brilliant film because he considers it a far more personal work than much of Scorcese's previous dramas. Both he and Scorcese grew up as Catholics pre Vactican II where hellfire was part of eternal damnation was everywhere. It clearly affected Scorcese emotionally, maybe to this day. One point after his divorce he said to Ebert: "I'm living in sin and I will burn in Hell." Ebert asked if he really believed it: "Yes." he said.
It may not compare to the majesty of Raging Bull or Goodfellas or Taxi Driver or the films that are considered Scorcese's masterworks but Ebert makes the argument that it is one of his most personal and may show how he sees the world. Perhaps so much of the controversy is not just because how the film portrays Jesus, but how it portrays Judas. Judas is shown as Jesus' closest friend, who instructs him along the way, and who even his betrayal is something that is practically authorized. Harvey Keitel is another great performance and maybe you should consider it the way Ebert ends his review: "Maybe Christ is the talent, and Judas is the director.
Food for thought