I will need to vote for FS2. Everything just seemed so much deadlier and more mysterious.
You have beams, flak, better and faster blobs and fighter weapons, bigger bombs, heavier and quicker fighters. All these things make every battle a struggle to survive, and makes every bomber a threat, and every approach to a cap ship or fighter group a tactical decision. In FS1, cap ships were more props then threats - just a bunch of weak blobs that you need to protect sometimes.
Then you get the story: "What is Bosch doing?" "Should I be concerned that the Iceni seems to keep escaping?" "Ooh, what's through this weird gate thing?" "Oh **** Shivans." "What are the Shivans doing?" "Oh **** a Sathanas." "Yay, Sathanas is dead, good job all." "Oh sweet ****ing **** more Sathanas!" "What are they doing?" "Oh, that's what they're doing. FLEEEEEE!" All very mysterious and emotional.