Possible spoilers below, but I think most people know what happens anyway... and I'm going to be vague. =P
Admittedly, I haven't played FS2 yet, but after beating the FS1 conversion... it's going to be tough to find a game that had atmosphere that excited me like FS1s did.
The way the game starts off fealing like you're doing things that are perfectly normal, and then you get the Shivans. Terrifying, unstoppable, unbeatable.
And you kill one. And it's thrilling. (At leat, the first time I killed one without having to use the reticle... just spamming Fury's, I was elated.)
And things seem to pick up... at first. And then the game spirals downard, all hell breaking loose around the Lucifer and HoL. The way the events play out, and the briefing voices, really make you think, "Oh ****... We're doomed." It really get's desperate. Especially as the missions get harder and more hectic.
Couple that with a joystick, and the game is one of the most immersive I have ever played, which is saying something since my imagination never lends itself to immersion. =/ I'll be amazed if FS2 even comes close, when I get around to playing it.