To be brrrutally fair, none of the last WoD missions were actually amazing, design wise.
Nonsense! Flying into giant motherships to blow them up were always talked about but never really done before! And why would I
steal borrow the idea for JAD:XA if it was so bad! (Also that asteroid beam gauntlet was so
amazing)
I've got too many other fine examples of FreeSpace mission design. Real quick, the Antagonist's final boss: your skill with all your accumulated abilities and weapons are put to the final test. BP:AoA, Forced Entry, which is like the whole of FreeSpace in 1 mission. Running from Shivans, fighting Shivans, mysterious Ancient Knossos, beams everywhere. So fine.
But I think the best two linked missions for me was in WiH, For the Wrong Reasons and What Binds Us.
In the first one, the tension is ratcheted up so high when you're "dogfighting" against the gefs. On my first play through I actually pulled the trigger too early, starting the firefight. I really didn't want them to get the first shot off. Alas, things didn't turn out so well and I kept my cool on the second run through. Then on What Binds Us, we're placed into almost the same situation, mock dogfight, look but don't touch! And then the feelings that maybe we could just put aside our differences and end the war. Until the UEF frigate arrives and grinds everything into dust. You just expect things to go so well like the last time you held off the trigger, but they don't. So tragic.
EDIT: Also, Between the Ashes, demo: first mission. Keeping those civvies quiet. You know what I'm talking about.
Too much to list!