Why bother with flashbacks? I'd like to see a reboot movie that opens with a pre-credits sequence of Ma and Pa Kent in Smallville, the crash landing, finding the child, etc, a 10 minute sequence or whatever... then you roll credits... movie 'proper' begins with adult Clark arriving in Metropolis. Simple, to the point, gives you the origin, but doesn't spend an hour rehashing the first hour of the Donner movie. The crash landing in smallville is one of those iconic sequences that you can show over and over again in any Superman incarnation and it never gets old as long as you don't drag it out.
Then you can do some fun sequences where we (the audience) 'discovers' his powers one by one in Metropolis.
Sort of like how in Hellboy the movie started with a WWII (?) era sequence, then 'forwarded' to present day for most of the movie. Actually a lot of movies do stuff like this.
Of course, i'd be using the more modern "post-crisis" continuity (Pa Kent is still alive, Luthor is much more of a public persona, who feels its his duty to protect humanity from Kryptonian invaders, his villainness really stems from a hatred of "aliens"). In fact, I'd take a lot of cues from the 90s Animated Series.
As far as villains go, there are some good options:
-Metallo (cyborg with a Kryptonite heart)
-Bizarro (maybe re-imagined as a Luthor Frankenstein experiment gone wrong)
-Parasite (his powers are a credible threat to Superman)
-Braniac (integrated with his origin, a la animated series)
It's important to finally break away from the 30-year-old movie. A somewhat new look for Superman, even stop using the John Williams theme, no more shades of Hackman's Luthor, a new asthetic, no more dour emo-Superman from 'Returns, no more "real estate" based plots. There's an entire generation of people who've never even seen the Donner Superman. People will be fine. Well-made big-budget blockbusters make money. They will go see it.