I agree with bits of this. Actually, I agree with most of it; I just think FS2's atmosphere and writing outweigh the rest.
Yeah, FS1's ship design was better. FS2's isn't bad, but the first game just had more...inspiration? to it. I have to say I adore the Typhon. I like the Hatshepsut, too, but that's mostly just because of the MediaVP redesign. The original model was pretty much just two hunks of beige connected by a hunk of grey. (Although it was a decent design regardless.) (I'm getting off track.)
On the subject of Shivan craft: I personally find the second game's Shivan ships more visually appealing, but I think that, "objectively", they are more generic and less original. Second-incursion ships have all those spikes and things, which is pretty standard for evil death aliens, as opposed to the sort of blunt, squarish sensibilities of FS1-era Shivan ships, which probably had more artistic merit.
And yeah, I think FS1's music was marginally better, if only because of Spook. (I love Spook.) On the other hand, FS2 has Joshua (and Leviticus, to a lesser degree), but I think FS1 wins out overall.
It's just...the voice acting, and mission design, and writing. It never feels like anyone cares about any of this. "Yep, an unknown alien race just showed up and is now seeking our extinction with invincibility shields and weapons we've never seen before. Yawn."
(The exception is the opening cutscene, which is awesome.)