I'm going to be honest, even though this point you're making, about the importance of editing and of prioritising the important scenes and of understanding the script, is obvious once you explain it, I don't think I was explicitly cognisant of it beforehand, and that may be the case for a lot of other people.
It's a great point -- but I'm not sure it implies to MoS.
Regardless of whether or not Snyder understood the story, it's not clear that the story was that dynamic that it would have benefited from a higher talent "understanding" it. I still think the script is subpar. I think if it weren't for Snyder elevating this weak script with good casting, acting, visuals, use of sound, sense of epicness, et cetera this movie might have scored 25% on RT, like Green Lantern did where the direction was as bad as the screenplay. If you go back to the reviews, nearly everything people liked about MoS is independent of the script, the only exception were that Clark's last words to Pa Kent before his death were "you're not my real dad".
I read your posts as suggesting that if Snyder was better at storytelling he would have better understood the strength in Goyer's script and polished it better. I'm more inclined to think that if Snyder was better at storytelling he would have lobbied for a page-one rewrite, assuming that he was allowed to do so.
The story we saw on screen is one where Clark never speaks in sentences longer than 4 or 5 words and barely says much at all, one where he's mostly reacting to what other people are doing/saying rather than being the source of agency himself. It's one where Jor-El tasks Clark with the mission of bringing back Krypton one day, but Clark ends up frying all the innocent embryos with heat vision. The whole codex plot point really doesn't make much sense at all, quite frankly, it's a less functional McGuffin than even the one in GoTG or in TDKR, and that's on Goyer.