Absolutely, EVERY mission in Wing Commander III 3DO is different. The entier game was remade to better suit the console; the mechanics were redone so it was more 'arcade': it's easier to shoot down enemy ships and so there are a lot more of them. The PC version is a different experience, with fewer fighters/capital ships that are harder to kill.
But the missions are just /different/ and playing the one you haven't is like getting fifty more Wing Commander battles you haven't seen before. My favorite example is the Tamayo scramble mission. In the original PC release you defend the Victory against four waves of bombers... and in the 3DO port you defend it against an enemy destroyer and her escort fighters!
The PC version also looks much better. The 3DO port had its own engine that looks sort of like a cross between Wing Commander II and Wing Commander III VGA. The PC's SVGA mode is much, much sharper.
That does it, I'm searching hell and highground to finally experience 3DO WC3. I'd be less of a fan if I didn't. The arcade style and brisky engine sounds sweet.