1.) Rather than the colorful, vibrant Smallville scenes in STM that establish Clark as having an extremely strong relationship with his adopted parents, there's a flashback to Clark, all alone, discovering his powers. Then flash-forward to Clark, all alone, on the farm. Oh, and his mother telling him: "Even if you are the last, you're not alone." Uh-huh. The whole message of the film is that Kal'El IS alone and will always remain so.
2.) The fortress of solitude scenes in STM, where Clark learns who he is, are more or less parodied in SR when Lex, Kitty and the other henchman arrive there and are somehow able to jump-start the crystals and Jor'El's presence. Kitty: "Can he see us?" Lex: "No, he's dead." The glib, mocking tone here more or less sums up the film's attitude not only towards the original Superman film but the Superman mythos in general.
3.) Kal'El's visit to Lois' penthouse in STM is re-created in SR but takes all the wondrous, magical aspects of the original scene and replaces them with a cold, cynical feel that sucks all the humor and warmth from the Donner version. STM Supes: "You really shouldn't smoke, Ms. Lane." SR Supes doesn't bother and just snuffs out her cigarrette like the glorified stalker he is in this film. Their flight together has a detached feel which is full of contempt for the scene it's based on. Lois and the entire Earth forgot Superman. There's no reason why he should love her or anyone else.
4.) Instead of putting Lex Luthor to rights in SR the way STM Supes did, SR Supes is nearly beaten to death by Lex and his henchman, stabbed by a shard of Kryptonite and then more or less pushed off a cliff to drown. And the only reason SR Supes confronts Lex in the first place is because "You have something that belongs to me," meaning that Lex stole his crystals/Jor-El's message. That's it. There's never any mention of Lex's schemes, his putting Lois and the rest of the world in danger, or even Lex's having escaped from prison. This is by far the weakest, most cynical, most anticlimactic resolution in a "superhero" film in the entire history of that genre.
5.) The misogyny that's present throughout the entire film. Women are either peripheral, unlikable or the target of cruel jabs. There's Lex's benefactor/victim Gertrude...there's Lois Lane who's pretty much a b**** throughout the whole movie, there's brainless Kitty (and yes, I know she's based on Miss Tessmacher but as far as I can recall there were no scenes of Miss Tessmacher's suffering at the hands of Lex being played for laughs) who despite being saved by Superman does nothing when he's trapped by Lex.
6.) Probably the final nail in the coffin is the scene of Kal'El being left to drown and Jor'El's words: "Even though you have been raised as an Earthling you are not one of them..." hitting home the message "Look, Kal'El is left to die and no one cares". Jor-El's words were repeated in one of the final scenes of STM, too, they were: "You are forbidden to interfere..." in earthly matters. That was right before Supes literally moved Heaven and Earth so he could save Lois Lane's life. Once again, SR takes the Lois/Superman relationship and rips it to pieces. Just in case there's any doubt, the SR scene takes place right before Lois saves Kal'El's life by jumping in the ocean...but only because his alien son spotted him there in the first place. After Kal'El is resuscitated back to life, (but only before he dies again ten minutes later) he once more valiantly sacrifices himself for Lois, Richard, Jason, and everyone else who couldn't care less that he's about to die for them.
7.) These are some reasons why fans hated SR, but also why many fans, viewers and critics didn't pick up on the filmmaker's contempt for the character mythos. In many ways the film feels like a re-make of STM, because so many scenes/lines are "repeated" in the 2006 version. But this is anything but a "fan-film".
As said earlier, a much better definition would be "parody."
I'm glad for anyone that could enjoy SR, and in fact I liked parts of it; but this Superman bore little resemblance to any other I've seen before, and the premise still doesn't make any sense to me. (Can anyone tell me why he left Earth for five years? Anyone? And I mean a reason that makes sense.)