The first flight was very emotional. I don't know what you were watching but I thought it was cute that Clark was attempting to learn how to fly and was grinning like a mad man when he finally did it right and was heart-warmed as he was smiling doing so as he was living the dream. Hans Zimmer's soundtrack further added to it and gave it a good backdrop.
Oh yeah I definitely agree with you on some parts. Zimmer's track in the scene without fail gives me goosebumps every time I listen to it, for me it's in every way a spiritual successor to Williams' theme, without being a theme itself.
I guess the flight scene isn't my issue, it's how little time we have with Clark before we get to that stage. It's like, if Bruce had become Batman within the first 5 minutes of Batman Begins, it wouldn't have been such a huge deal. But because we go on such a journey with him, getting to know what motivates him, by the time he finally takes on those thugs and utters 'I'm Batman', I'm ready to jump out of my seat the pay off is so good.
For me, the build up is nowhere near as strong in MoS. We barely begin to scratch the surface of Cavill's Clark (how many lines does he have before the Fortress with Jor El, a 'thanks' on the boat, a line or 2 in the bar?) before he's suiting up. If anyone's wondering why this film was met with such a luke warm reception by much of the GA, I'd guess it was for this reason, the film didn't give people someone to connect with. The bar scene is great and begins to do this for the audience, but in my opinion it's not enough, there needed to be more in the script.
With all the quick cuts leading up to the flight scene, rather then an actual story, it felt like it was a montage to get us past that plot point quickly before getting to the real meat of the film, when for me my emotional investment would have been in those moments leading up to an epic suit-up. I still love the film, but a huge point of that is because I love Superman in the first place.