I think there's definitely a strong current in older circles to see MOS as inferior because it breaks from the mold they see for Superman. It's similar to the break between comic fans over Superman and his world, but a bit more entrenched because of how ground-breaking the first film's imprint on pop-culture was. The nostalgia factor also gives it an edge for people who have grown up with it as the personal pinnacle of comic book movies.
I do think it's important to note that there's a major disagreement over the philosophy of Superman's powers and the depth of the Science Fiction in the stories. "Adherents" of the Donner films and their portrayal have a strong believe in what "adherents" of more modern stylings of Superman consider weaknesses or jokes of the style: clumsy, comedy-centered Clark Kent portrayals, liberal use of deus-ex-machina, excessively inconsistent portrayal of Superman's abilities, a weaker supporting cast in terms of their actual capabilities and development, a fanatical devotion to the status quo, and a greater focus on fantastic approaches to the whole world.
For instance, someone like me, who is seriously biased against those traits, sees the ending of MOS as a fantastic and visceral rebuttal of what I perceive as weaknesses to S:TMP and SII. I believe that turning back time and amnesia kissing away a subplot ruins the conflict the films' develop and betrays the point of a Superman, whereas they see the destruction of the city and violent climax as a betrayal of Superman's message; the reverse is also true. I think that a klutzy Clark Kent is a charlatan, and that a shallow Daily Plaent staff is juvenile; they think that a subdued and stoic Clark is bland, and that the Palnet has lost some of its charm without its quirks.
And those differences can radically shift the way you see the film: a lot of older critics despise the violence, and never mention the scene where Perry and Steve try and save Jenny, while I am finally satisfied to see Superman be a badass and actually think the Planet staffers standing together gives the film a heart that I never saw in S:TMP's human characters.