The problem is that the big chunks of Donner's version were unfilmed when he was let go (and I seriously doubt the Salkinds take on that), and they'd already decided they'd have to rethink the ending when they came back to finish II, which obviously didn't happen.
I look at the Donner cut as sort of a historical artifact, a partial reconstruction of what was intended, to give you an idea of what the film was supposed to be like. I think, perhaps, the problem is that it was released like it was a complete alternate cut, instead of the incomplete artifact it is. I'm not going to deny the editing is sloppy and other faults of the storytelling, but the point was to show what Donner wanted, a style mostly incompatible with Lester's.
Personally, I find Lester's version of Superman II unwatchable for its broadness and its own sloppiness (you want continuity errors, it's full of them) and its bad taste.