I know what you mean. This focus on his 'destiny', while it makes for a good story, is not a definitive Superman story. I think the new film will at least focus on Clark inventing his own destiny a lot more than from what we've seen in the film franchise and in Smallville.
I really hope so. I think it makes him a lot more likeable when he's choosing to do something good with his powers.
Whenever you have the 'it's his destiny' plot, this kind of self pity comes with it. Like what Buffy used to get like sometimes - why me, why do i have to give up my life to save the world, and never reap the benefits of being the hero.
But when this is something he has chosen to do, there is no question. He couldn't possibly not help people, he is happy to use his abilities in the best way he knows how.
Though, I disagree with you about the latter - Jonathan and Martha Kent were beautifully written on the show, and their influence in making Clark become who he is was more instrumental than Jor-El's. The way I saw it, even after S5, it was Jonathan's death that drove Clark deeper into his actions, made him drop out of college, spend more time in Metropolis etc. Yes, its a radically different origin story but it kept the themes intact. Jor-El's prophecy is still there and does become an important plot point too, but its no longer the only reason why Clark becomes Superman. .
I think the Kents on Smallville were incredible, don't get me wrong. Such strong characters, and you could really understand how much of an influence they are on Clark because their personalities were so powerful.
But as I said above, it's the 'why me, i just wanna be normal, i feel pressured to live up to people's expectations of me' stuff that Smallville was occasionally full of, and that I hated. It's also that stuff that ruins characters like Chloe. She became the voice of 'it's your destiny', and started to become quite annoying.
Also, I think the point of the original CR film was that Superman is who he is, and Kent's the fabrication. Since Goyer, the man who wrote Batman Begins, is involved, I think we might see that highlighted once more. But this is just a guess. So far Goyer spoke a lot about MoS and wanting to make it 'modern, action-packed, and fun'. So for all we know, it might be something else entirely.
.
Any suggestion in the flim, that Clark Kent is a fabrication, will severely annoy me. IMO Neither PERSONA is a disguise... just aspects of Clark's personality played up or down. The disguise is the glasses and the posture when he's Clark, and the flashy coloured suit and confident stance when he's supes.
Opening sequence with Superman, but not showing him completely (as a teaser/flash-forward)...then start with Clark as the new reporter at the DP a few days earlier, then we go back to the opening sequence in full as Superman's official first appearance.
As for the 'why/how he became' stuff....leave it mostly a mystery in the first film, like it would be to the people in that world, as they somehow come to grips with this otherworldy and fantastic new phenomenon.
I do like the idea of getting a feel for how the people of that world percieve him. But I want the story to be predominantely told from his perspective. I want to see what it's like to BE Clark Kent, as well as what it's like to live in a world with Superman as your hero.
I think the why/how stuff is important in understanding his perspective, and his feelings about being Superman. In fact, I think it's essential. It doesn't need to take over the whole movie, but I think in needs to be there. That's all I mean by an origin.