Re: Would you do anything differently in MoS?
First thing I would do is get rid of the flashbacks and have them be the first act of the film. My biggest complaint other than the pacing is that it feels as if the film lacks a second act. It would be as if Bruce gets back to Gotham in Batman Begins and then Ra's al Ghul attacks right after. The start of the film up until Clark gets back to Smallville feels like Act 1 and then everything from Zod's message to the end of the film feels like the Act 3. Something is missing in between. We never really see the public's reaction to Superman (only the government's reaction, Perry's, and Lois'). We never see whether or not Jonathan Kent was right.
My theory is that originally they weren't going to do the origin in flashbacks and have had that be the first had with adult Clark travelling being the second act and then finally with the Zod attack being the final act. However, they probably wanted to avoid the film being compared to the Donner film (since the first film used that exact formula) so they stuck to the Batman Begins layout.