I like it but I recognise that it's flawed. I think that Singer made a mistake in assuming that the audience would remember the first two Superman films over 20 years later; sure, geeks like us know them and many people of my age have seen them. But to the general audience, it made the story and its background a little hazy. The whole 'semi-sequel' was a bad idea (and I say so as someone who at the time was against another origin story).
The movie is slow and sombre; I personally liked its tone but was surprised by it. It's pretty clear audiences wanted something more upbeat, perhaps in the vein of Raimi's Spider-man movies or the Iron Man series (which hadn't yet been released). Additionally, there is a surprising lack of action for a modern blockbuster movie. I personally think that MOS perhaps went overboard in its action sequences and I like how Superman in Returns spent as much time in Metropolis saving people as anything else. However, when the climactic action sequence is basically Superman pushing a big asteroid into space, well, audiences may feel short-changed. I also think that another Lex Luthor landgrab plan was a bad idea, though I think Spacey channels a malevolence in his Lex that the great Gene Hackman never captured. The scene where he sticks the Kryptonite blade in Superman's side is quite shocking.
The idea of Superman returning to a changed world was intriguing but I'm not sure too many people were interested in seeing how the Superman-Lois-Richard-Jason dynamic went in subsequent movies.
I also love Brandon Routh's take on Superman, which I think segues effortlessly from Chris Reeve's take. I love Henry Cavill's version too, but I still think it's a shame Brandon never reprised the role. I think this movie handles his humanity and personal conflict better than MOS and little scenes like Martha Kent outside the hospital, unable to get in, as she can't reveal her son's identity, are more touching than anything in any other Superman film.
When WB said that they were going to reboot the series and wouldn't make a sequel to SR, they said that it could be viewed as 'a bookend to the Donner movies.' This is at once Hollywood spin and actually a pretty good way of viewing it - a one-off take on Superman and closure to that take on the character. When MOS comes out on DVD/Blu-Ray, I look forward to watching them closely together at home - I think they may complement each other in some ways.