I'm looking forward to what you guys come up with.
IMO, just focus on building strong team interaction. Big battles are hectic, and it ultimately comes down to the ability of a team to coordinate. If it's nothing but a big FFA in game, even with Discord, it's just going to be a giant mess to get involved in bigger battles. In-game squads, formations, target designations, even having some guy in a cap ship playing as admiral giving orders and creating waypoints are a few examples I could think of. Allow squad leaders to build on that.
One HUD idea I think may help in this regard is to have a form of complete transparency from inside the player's cockpit. So once activated, a new HUD allows the player to have a completely unobstructed 360 degree view, and can easily see where the rest of the squad is.
As to a sea of projectiles, such is war.
Otherwise you'd have to find some way to encourage players to split up and nearly exclusively fight in smaller groups. You could do this with having a very quick turnaround on asset ownership, forcing a very quick reactionary force to intervene. But then you'd have no really big battles, which would stink.
As I said, I'm looking forward to what you guys come up with.
Just my two cents.