I think the problem with keeping Superman in the real-world is, that you can't have any real physical threats for the lager than live character that he is. Sure, it works for Batman, but telling good Superman storys is just a whole other challenge. Also, i don't really see the problem in basing Superman into a more scifi kinda of world. I mean, they do it in the comics too and that's the source material after all. And it's not like that would mean you'd have to go in a stupid popocornmovie directon with the character. It's very well possible to do a actionpacked movie with a lot of scifi elements and still combine it with deep storytelling.
As far as the whole Batman Begins world/Superman Returns connection goes ... i don't really see that. To me, it didn't look like that Superman Returns could be based in the same reality as Batman Begins. In fact, i don't think it would make sense for any other DC-Superhero to exist in the BB world. And that's why i have to agree with you, they should just keep all the solo-movies as well as the JLA in separate universes, so that they can model them after the individual needs of every hero...