I wouldn't say Superman Returns was completely it's own thing. For a good stretch of the film, it was a reprise of the original film. Eventually, the film evolved into it's own thing.
I still think that film works as Superman III to Donner's first two. It closes the thematic loop. The biggest problem fans had with it, in my opinion, was that Singer spent 209 million on a love story...when what the fans have longed for was a modern version of the character after having been away so long.
But, I still agree with Singer's premise. The origin of Kal-El, whether from comics, TV, or from the original film, is so hardwired into everyone's DNA, it made sense not to do a hard reboot and do the origin again. It made sense to just pick up where we left off. And had Singer got his sequel, I think we'd be in a totally different situation right now.