Remember the plotline - is the character participating in events that drive the plot forward, in most missions? In Blue Planet, for example, look at how many of their missions take place with plot-critical settings, in the strategic scope of things.
Age of Aquarius' plot was awesome because, after the first two or three missions, it became a full-afterburner ride through a shivan-infested parallel universe, just trying to stay alive. All of that happened over the course of (probably) a week or two.
War in Heaven's plot was equally awesome because it maintains the same pacing. It starts out at a reasonable rate, defending convoys and ambushing capital ships, escalating into a full-on attack on Earth, and into a series of plot-critical missions for the entire second half.
However, for a 100+ mission campaign, I fear that you're going to try to put the player through every single mission in the war, and I'd strongly advise against it. Age of Aquarius had a small number of GTVA ships involved strategically in the plotline (only the fleet they sent through the gate), and the actual duration of the 'war' was limited by how long they stayed in the parallel universe. And even at that, the player ended up flying from the Temeraire for the majority of the campaign, largely missing out on the Orestes' share of the action. Most campaigns with a full-scale war going on, with hundreds of ships on each side, across countless battlefields - how much of that action does the player see? One percent? Maybe two? AoA put the player in roughly 50% of the action, maybe a little more, because of the short duration of the war and the very cool circumstances.
My point is, even under the best of circumstances, do you think you will be able to keep the storyline moving forward at a reasonable rate, when the campaign is a hundred missions long? Are you going to be able to build enough unique missions to pull it off? Blue Planet worked because it paced itself. I didn't mind the two or three slow missions up-front - but assuming the same proportionate pacing, yours would take up...ten? Maybe fifteen missions of relative calm up-front - and personally, after about four or five, I'd get bored.
Similarly, the action begins to lose scale when you just go full-afterburners for very long. Look at all the tricks the BP team used to keep AoA interesting, in the face of their full-afterburner plotline. The chasing down of the Duke, and subsequent discovery of the Sanctuary? Then the fleet moving to the Knossos portal? Then getting jumped by a Shivan armada, to have the Vishnans arrive in time to save them? The few missions the player flies WITH the Vishnans, culminating in an assault against the Lucifer and a reunification with the Orestes? Then a fleet-wide reunification over a Sathanas-kill? And finally a showdown between the Shivan and Vishnan super-juggernauts, and a fleet-wide escort mission back to the GTVA's native universe?
It begins to stretch the limits of how much action can be crammed into a campaign - but it is executed extremely well. But even Age of Aquarius would be boring if that plot material was stretched out to cover 100 missions. A hundred-mission campaign seems far too prone to either boredom or action burnout. Shock is only shocking when used sparingly.
Now, I bring this up not to tell you that it's impossible to make a good 100-mission campaign, but that it will be both extremely difficult to do well, and that it's going to cost you a buttload of time in FRED. In all honesty, it would probably be a better use of time to make a shorter campaign.
If you haven't downloaded and played Blue Planet, I'd highly suggest you do. I'm opening their missions in FRED, and learning how to FRED from them by observation. It's a great resource for learning how to put together both simple and complex missions.
