hehe, well once we get going we'll need players after all 
Right now we're still trying to figure out what IS possible in the engine (size of fleet engagements,
capships in multiplayer, etc.) so it's still an early phase.
Fair enough.
FS2 has a couple of major size limits. You're limited to around 100 ships in a mission (more than that will crash the mission usually). There is also a limit on the number of subsystems that can be present. Obviously big ships like the Colossus have a lot more subsystems than small ships like fighters do so a large number of them can drag the number of ships you're allowed downwards very quickly.
A recent addition to FS2_Open allows you to spawn ships and you could probably use this to get around the limits somewhat. Be warned that once you have too many ships in a mission the collision detection routine becomes unable to track them all and you end up with shots travelling straight through ships.
FS2 multiplayer games can be split into 3 types. Cooperative is probably useless to you from the sounds of it because everyone is on the same side. That leaves you with team vs team and dogfight (everyone fights everyone). The problem with dogfight is that event scripting doesn't work except at a very basic level. You can basically turn beams on or off, make ships play dead but not much else.
TvT on the other hand only gives you 2 sides. If you wanted 3 way battles I think you're probably out of luck unless it's possible to do it using co-operative mode and changing the iff of beta and gamma wings. I've never tried this so I've go no idea whether it can be done or not.
Depending on how you're planning to run the campaigns I'd probably reccomend making a series of template missions (fighters only, skirmish, medium battle, big battle etc). Make the templates with several ships in them and then simply edit the missions with the names of the players capships (if you're naming them). If the players have different numbers of ships it's not too hard to simply edit the mission to give some of the capships a false arrival cue (Which basically means they'll never warp in).
The other possibility (depending on how long you have to prepare the mission before a battle has to be fought) is to simply prepare the missions from a more simple template and add the ships as you need them. That's a cruder way of doing things and is more prone to someone forgetting to beam enable a ship, have it retreat when damaged etc though. That said even a beginning FREDder could knock up a TvT mission from scratch in under an hour. An experienced one could do it in under 10 minutes if it's fairly basic. Once you have a template it would be even quicker.
If you've got any more questions just ask away
