In Freespace 1 it felt like a game of chess, with a finite amount of resources, and even the loss of pawns was felt. In Freespace 2, strategy was mostly "We're going to throw a fleet at it and hope it goes away."
But that's not a gameplay issue. It's a storytelling one.
As long as we're waxing long on atmospherics, to be blunt I've seen scenario packs for Harpoon Classic that tear either FS to shreds on this. One I recall in particular was basically the chronicle of the Royal Norwegian Navy during a general war between NATO and the Warsaw Pact. Even with Harpoon's very serious storytelling limitations (basically, all you got was the scenario-select screen briefing texts) and being unable to really track the status of ships from scenario to scenario, it conveyed the feeling of being overwhelmed that FS1 was reaching for (and admittedly, achieved) far, far better. Some of the official expansions were single set campaigns as well, and they were good; good enough I remember them more clearly than any of the missions for either FreeSpace. (I can probably name more Harpoon Classic scenarios then I can FS missions...and it's no accident a number of my own borrow their names; FS1 and FS2 often took a turn for the too obscure.)
Now, this isn't totally tangential. It brings me to the real problem with FreeSpace in this sense: scale.
FreeSpace, both of them, is trying to tell a story from a viewpoint
where you can't see its shape. The view from your cockpit is a tiny one, encompassing very little space or time. This is partly, or perhaps entirely, its own fault, because FS has the tools to widen the viewpoint. Harpoon Classic does it with nothing more than its own equivalent of command briefings. (And that's all it has!) FreeSpace 1 came closer to the Harpoon model with its CBs the FS2 did, because it kept you more informed on the goings-on outside your tiny viewpoint, and consequently, it better conveyed its choice of atmospherics and scale. FS2 is replete with ships you never see again, cruisers and even destroyers going up in flames, and so on because the designers veered in a different direction in trying to convey the sense of scale and atmosphere. Instead of trying to create the illusion of a war off the screen, they tried to compact the war entirely onto the screen. This was seriously detrimental, as doing so gave the player ridiculous power since they're always present and usually involved and lead to the jadedness WMC aludes to. But there is worse.
Alpha 1's experience was supposed to be, well,
everything. But they couldn't make it that way because of the scale of the view from your cockpit; that Alpha 1 missed absolutely nothing in a campaign as large and as long as FS2 portrays is impossible. They tried to make some concessions to this early in FS2, and there was an occasional spasm of it later on (the command brief detailing the NTF's suicide run to Gamma Drac comes to mind), but in the end they simply couldn't accomplish what they set out to accomplish storywise and cram everything into the view from a fightercraft cockpit. Even making the effort seriously damaged conveying the story to the player.
...And I think I've broken some sort of cosmic writer's law by finding a situation where you should have told rather than shown.