I don't think their crystal tech works that way, just toss a crystal and have it morph into whatever you want. Krytonians are xenophobic, they stuck to their planet and never really ventured out into space after they became xenophobic so didn't have space tech ready to go. Think, if you watched the cartoons, Jor El tried to warn the heads of the Government there about the planet being unstable (but not that it was about to explode, just that it's unstable), but the council were entrenched in their superiority and could not believe such a thing could happen. So the other Kryptonians never really knew ahead of time such a thing was about to happen because the Council did not deem it a concern. So Jor El prepped some contingency ahead of time as quickly as he could without really knowing what would happen, then the planet started exploding and he had a ship ready to go.
There's other storylines where Kryptonians were bound to the planet genetically somehow because the Guardians or something, I don't know. Jor El found a cure for it and gave it to his son or something.
Another one was that they used to dominate space being extremely militaristic. Then the scientists took over and decided they should become xenophobic in some kind of penance. So they eradicated and banned spatial vehicles. This xenophobia became engrained into their society, so they never really left their planet. Jor El started to experiment with it and began questioning their isolationism and built a prototype. Then planet exploded, etc.
Or you can just chalk it up to comic book universe. You're being kinda over-demanding for something from comic-book universe. Why do you hate Superman so much? You seem fine with Iron Man and some of the others and not as demanding with them....