So many issues could have been resolved with a few lines of dialogue, but the writers apparently couldn't be bother. Here are some off the top of my head:
Superman's suit? Manufactured onsite by nanotech or some other fabrication tech. Presumably the super genius of Jor El could have the plans/patterns.
How the "bad" Kryptonians had superpowers without any weaknesses? Not super powers, but powered suits (think Iron Man).
Superman's fighting skills? Have something to do with whatever was injected into him as a baby, the potential of all Krypton or whatever. Actually, that whole fucking plot thread shouldn't have been in the movie.
Superman getting weak on the alien ship? Ship is irradiated with Kryptonite during the explosion that retardedly set them free.
He got weak on the ship because it was Krypton's atmosphere, it rids him of powers and his body is not used to it. The German (?) Kryptonian explained that. And he never showed any fighting skills other than brawling and punching which anyone can do given super-speed.
BTW, the plot hole of the Fortress of Solitude is false. The ship crash landed on earth many thousand years ago after the crew was killed while frozen in the chambers. It's explained the the prequel comic.