Perhaps I simply didn't put enough effort to "git gud" at Homeworld 1, but I liked the squadron-mechanic from HW2 better. It gave you a better chance to save your fighters during a battle. And the lack of the missile destroyer meant fighters and corvettes could actually survive around capitial ships. In fact, they're needed to protect against the enemy's strikecraft.
The paper-mache frigates, on the other hand, were a downgrade. They could NOT survive near capital ships, and they weren't all that effective against smaller ships, especially the vagyr ones.
And I'm with you on the story. It's a bummer. The hyperspace cores were suddenly magical bullshit, though it's never clear what's so special about them since all frigates and capitals can hyperspace fine without them. The prophecies were dumb. And then there's that hillarious mission where the bad guy goes through a portal and you have to defeat his rear guard before they blow up the portal. That portal lead to the MacGuffin that all the war and propecies were about... and the bad guy started the whole war because he knew he needed all 3 cores... he had one... you had the other two... If you'd have let his troops blow up the gate, he'd have been fucked. (Oh, and of course you make it through, kick his ass, and get your hands on the MacGuffin anyway, which is good because the bad guy pulls a planet-bombardment ships that can't be damaged in any way except by the MacGuffin right out of his ass.
Yeah, could've stood a few rewrites. Cataclysm's story was kinda corny, but a lot better.