Wrath of Khan is the perfect analogy for the situation we Superman fans find ourselves in right now. Like the first Star Trek movie, SR was a decent hit but was a flawed film that could have been a lot better. The biggest problem in both was a lack of action. Wrath of Khan corrected the course of Star Trek, and hopefully SRII could do the same for the Superman franchise.
It's possible, but after SR it's hard for me to have faith in Singer. This was his dream project, but in the end his fandom for the Donner film at the expense of the broader Superman mythos did the film in; it felt like a total retread. Basically, Singer hasn't proven to me that he has any original ideas - at least, any that aren't going to suck (Jason).
Ideally, what I would like to see in a SR sequel would be more of what I wanted to see in SR itself. That is, more depth to Clark, Lex using the Vanderworth fortune to start Lexcorp, etc. Seriously, the pre-Crisis Lex just doesn't cut it anymore. And if we can have a really amazing supervillain, then it'll all be good. At the very least, how about giving more lines to Brandon? Jesus, he had so little dialogue in SR that you just didn't really connect to the character at all. Making Superman the focus of a Superman movie is probably a better idea.