There is one thing I think FS1 did pretty well, or...at least...sort of tried to do well, which was small-scale stuff. That is, in the sense of building up a single Aten cruiser as a credible threat and a Big Deal.
Unfortunately, it entirely fails to sell the apocalyptic horror of the Shivans, which kind of wrecks the experience.
(Also -- and this is sort of new-thread material -- but I feel like there's a distinction between a "mission" and a "battle", and in a game about a "Great War", you need at least a few of the latter, which...there kind of aren't. This is related to but not synonymous with the BoE concept -- a mission being a battle is more about presentation than scale. You could easily have a proper battle with just a couple destroyers and cruisers, if you set it up correctly -- portray them as unified battlegroups that meet for in a pitched engagement. I think part of the issue is that so many engagements in FS are running affairs, where the objective is to get from one place to another, which detracts from the idea of it being a proper battle.
I think what got me thinking about this originally was the opening cutscene of FS2, which drops you into "THE BATTLE OF DENEB". Now, it's not as though those sorts of situations don't happen in-game. If you took a few minutes of high action from one of the more hectic missions, it'd look pretty much the same. (Case in point: FS2's ending cutscene.) But it feels different, because the engagement comes together so haphazardly.
I have gotten horribly off-topic. Apologies.)