Hardest mission? *SPOIL*
For me, it was when you're going to meet Kress, and that Rheinland fleet uncloaks, I had some serious trouble then, so many missiles from those damn gun boats.
It was either that one, or the one when you assault the Arch, Governor Takkagi's base. That one was hard too.
I found the end Nomad ones kinda easy, because Nomads can go down pretty quickly, and because you have tons of cannon fodder (wingmen).