Hope this hasn’t come up before, I don’t remember seeing it…
Commodore “box” would be a non-weapon dingus goes in one of the square boxes on a ship. Would be optional–don’t add any, and your fleet is all one generic squadron anyway, controlled entirely by basic orders.
But with a Commodore one can then add ships to Squadrons (or task forces or sub-command groups or whatever Gratuitous term works best). These Squadrons could be given orders as a group (not much different than can be done now) BUT squadrons can also be given orders that relate to other Squadrons–such as formation, or escort, or protect. Formation, for example, could be used to assure two groups of your ships stay a certain distance apart–so long as both ships with the Squadron Leader box are intact (or, perhaps, the individual boxes remain undestroyed). Or maybe you want one big group of fighters to protect or escort a squadron, instead of just one ship…
If we’re feeling Extra Wacky we might imagine orders like “stay on my left flank” or “remain in the rear”–like a formation order, but the interpretation would be much looser, sort of like formation but with an escort range bar with the added tweak of being directional based on the facing of the commodore’s ship. Whoo. Would have to be sure to get that ship’s orders juuuust right. 
Or maybe instead of directional based on the commodore’s ship, the direction is entirely based on the map’s orientation–“to the rear” is always “towards deployment zone.”
Squadron Leaders could also have a function that helps prevent “target overkill” by groups of ships, ensuring that if ship A in a squadron hits target Z with a tractor beam, no other ships in the squadron would follow suit. I have personally found that doubling up on tractor beams on ships devoted to AA work is a waste of equipment at least 50% of the time, as the targeting thingy often selects the same target. Probably more than half the time, actually. Dicey thing here is to be able to tune the weapons one wants to avoid doubling up on–cooperatively spamming a target with beam weapons is usually what one wants to happen. Perhaps if the algo was reasonable to craft, a Squadron Leader could help avoid overkill–massive salvoes that target nearly dead ships. Probably too complicated, that last, but why not dream. It is the suggestion forum.
This sort of thing might also serve as a more convenient way to give orders to all ships in a squadron–the typical everyday orders, like cooperate–as an option; one would of course want to be able to do it the old fashioned way, too.
I’m sure if this sort of thing were thought about more, more applications for it might be discovered.
Now, I hear what you’re saying. “But Red, we can already do most of this stuff with regular orders!” Well, some of it–but with this I can envision doing up–in a big map with lots of cash–three squadrons, battlegroups, task forces, whatever, and giving them complimentary orders so they form a large formation that will remain generally intact so long as the commodore boxes are intact. Faster forces on the wings, but not getting too far away from the center, which is speed-controlled through ship selection to set the desired overall pace.
Perhaps you’re like me and consistently start forces in one of the two corners of the deployment area–why? I do it to help control the future behavior of the ships I’m deploying. There is one less variable in possible travel direction–they can go forward or toward the center. Ships deployed in the middle have three general paths, and one might not like the results when some ships go haring off in the wrong direction. Something like these squadron-level orders could help make the entire map more palatable to more players.
Or maybe I want–REALLY want–ships to stay in a line, even if the enemy is not spread across the entire deployment area. Sure, the formation order will do that, but not in a real organized way, and it requires a lot of shift-f ing, and the destruction of a ship can unravel the plan catastrophically. Any ship, not just one “important” one with a commodore on board.
If Cliff is working on some kind of campaign mode, there are several applications for this idea there, which I leave to your imagination.