I was actually pumped to discuss this, but got quite a few lolz from the thread instead, win win.
But srsly. I care more about atmosphere then anything else, and the grinding dread of knowing that you're fighting in the face of Juggernaut himself, only delaying your doom... propels FS1 to top score imho.
The Sathanas never scared me like the Lucifer did. It was something destructible. We could beat it. It just was really really powerful.
For most of FS1, the Lucifer was invincible. It wiped away opposition with almost no effort, and no matter what victory you could take, you always knew the Lucifer was there to destroy you anyways. Much better for the story and atmosphere imho, although I'll give FS2 props for being more action packed (better mission design in general and beam cannons and flak).
The nebula was cool.. but I hated it. The blindness I think was supposed to create fear... all it really did was annoy me. The god damn lightning sounds piss me off after they repeat for the zillionth time