One of the things I felt that HW2 missed from the previous two games was how the gameplay affected the mood and feeling of the game. I'll give two examples.
The mission just after Karak is destroyed in HW1 is crazy. In the span of one mission, you go from fighting basic fighters and corvettes to assault frigates, ion-frigates, and a fricken carrier with a full compliment of fighters and escort ships. It creates the feeling much like the new BattleStar Galactica: you're a rag-tag fleet on the run from an enemy with a hell of a lot more stuff than you've got.
It also teaches you to never, ever send everything you have away from your Mothership. Which is a very good lesson to learn.
Cataclysm had a really great moment when you first encounter one of the Beast's assimilation ships. You send a force over to investigate, and in the span of maybe 3 seconds, all of them are assimilated and are now turned against you. It's a great combination of storyline and gameplay. In-story, your character is going, "WTF just happened? Oh crap!" But the player is doing the same thing, especially if they sent a few more ships than was asked for (as I did). Watching your fleet not merely disappear but actively turn against you when you know you don't have enough to stop them... yeah.