Things i would definitely do during the origin:
1) Give Clark a true childhood friend. I always felt that Bruce needed one and Begins gave us exactly that. I feel the same way about Clark. Give him Pete, or Chloe, but use different actors so that nobody comfuses the movie with that crap that is Smallville.
2) If one day you discovered you can fly, what would you do? Fly around the world visiting places. Fly over the Sahara, dive with the seals of the North pole, fly with a flock of migrating birds, fly over Paris, NY, the steppes, the Alps, etc. Personally its my favourite superpower. Imagine flying over all those places. I'd definitely put all that magic on screen.
3) Show Clark adjusting to Metropolis. His appartment and his hateful landlord, meeting people in the Daily Planet, etc. I loved how "Lois & Clark" explored details like that. Of course it was a weekly show and it had all the time in the world to do that, but still...
Now, to another issue: Lex.
Lex has been done to death, but you cant leave him out can you? Lex needs character development and i'd choose the comics and STAS path. Lex does a lot of charity work and is trully trying to help the world, but when after all his hard work and donations a man who can fly takes all the attention without so much as trying, he starts descending to the dark side. I'd use Brainiac as the first villain since he ties to Krypton and its destruction, and therefore the origin that the first film is all about. Meanwhile i'd show Lex descending to evil and i'd use him as the main villain of the second movie, with someone like Metallo or Parasite being the brawn to his brain.
Tell me what you think about my ideas.