I really liked both games. Played the demo of FS1 a long, long time ago at a friend's house, and fell in love, went out and purchased it. I was about to shell out $60+ on eBay for a copy of FS2 before I found Home of the Underdogs and the SCP. The Freespace series really is one of the best I've ever played, in terms of atmosphere and such.
I have to admit, I really liked the FS1 'hopeless' atmosphere- especially near the end, as Vasuda Prime was nuked, the Galatea was destroyed, and Earth itself was under threat. The idea of a inscrutable, indestructible enemy worked really well in this case.
FS2 had its 'set-piece' moments as well- Kappa 3 desperately telling Command to shut down the portal, the Vasudan destroyer trying to spearhead an expedition into the second portal before being vaporized, the moment the Lysander and Actium encountered the destroyer, etc. The Sathanas wasn't nearly as scary the first time around as the Lucifer, though. One thing FS2 does really well in this regard, is maintaining that sinking feeling in your stomach...'how many more of them ARE there?'. There are always these little clues throughout the camapign that point to a much greater Shivan presence than Command will let on to.
One thing that FS2 did really well, though, was gameplay atmosphere. I hated capital ship battles in FS1. The capital ships weren't that scary, their lasers were really kind of useless, and they were helpless against a determined bomber squadron. Having flak, beam cannons, etc. just makes it so much more epic, and actually gives capships a reason to exist.
As for the intros, I liked FS1's intro a LOT better than FS2's. FS1's was dramatic and very well-done. FS2's battle scene was kind of cheesy (maybe too much SCP goodness...I think that, with the exception of the hundreds of fighters, the SCP could probably render a better-looking scene in real-time). The laser that blew up the one Medusa looked like a solid plastic spear. And the narration wasn't that good, either...there are some really good quotes in FS1 and FS2, but I found the opening narration rather pointless.