These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Brilliance: The encounter between Paul and Jesus in the temptation scene. Paul writes in 1 Corinthians 15:14 that without risen Christ, all faith and preaching are in vain. Had Christ fallen to the last temptation, there would have been no resurrection and Paul's preaching, if it still took place, would have been a lie. Christ's crucifixion nullifies this and renders Paul's future preaching true.
Subverted in actual fact. The film was a box-office flop and in fact, pundits got paid made more money to decry the film on radio hosts and talk shows than Scorsese earned own box-office receipts. The box-office failure and the strong reaction it provoked, including Anti-Semitic outbursts(fundamentalists burnt crosses on producer Lew Wassermann's lawn, Wassermann was Jewish), made the film industry skeptical of bible films and religious subjects in general.
Massive letter-writing and boycott campaigns from various religious groups, most notably the Catholic League (who encouraged Catholics to never set foot into any theater which showed the film ever again), also didn't help the film's box office.
To this day, the film is still banned in Singapore and The Philippines.
One True Threesome: Jesus is implied to become one of these during the alternate future when, following Mary Magdalene's death, he ends up living with Mary and Martha, the sisters of Lazarus, and having many children with both of them.
Vindicated by History: Decades later, some hard right fundamentalist Christian sects like The Promisekeepers would eventually agree that the infamous temptation in the film would be precisely the kind of trickery that Satan would try on Jesus.
WTH, Casting Agency?: Willem Dafoe, known for taking dark, psychotic roles and looking generally Satanic, plays Jesus. Sergio Leone, at least, did not take it well.
"This is the face of a murderer, not of Our Lord!"
Scorsese justified this on grounds of averting Jesus Was Way Cool, wanting a Jesus who wasn't immediately charismatic and obvious in his message but someone who grew into his role and an actor who illustrated the conflict between being fully human and divine.
Also David Bowie as Pontius Pilate raises most people's eyebrows, but Bowie then turns in the most subtle performance of the film, portraying Pilate as intelligent, thoughtful and reserved.
It can be very alarming to realize that Judas is Mister White.