R.E. fleet engagements
This is why F&E limits fleets to around 10 ships with DN/BB/CVA command ships (and, as I remember, spending a command point could bump this to 11). Running a sixteen ship fleet WILL result in a lot of one shot-one kill situations, and should NOT be encouraged!
In SFC, I think I'd suggest limiting fleets to 9 (3x3), with the limitation that one size class 4 (DD/FF) ship is required for every larger ship, and one size class 3 or 4 (CA/DD/FF) ship be required for every size class 2 (BB/DN) ship (so you could have a BB, CVA, 2 cruisers, four DD/FF and a size class 4 scout).
And if someone wanted a fleet of 8 frigates with a CC, more power to them! In the 'yard' interface, the command ship you bought would dictate how many smaller ships you can have. The only time this would get tricky is if someone shot your CC out from under you and you had 8 leaderless DD/FF's. My guess is that the game interface would 'refund' you for the lost ships (perhaps with you picking which ships to send down the road) until you met your reduced command limits. Or, you could simply say that 9 ship fleets are always allowed (to save headaches).
Are the size class 4 ships effectively popcorn? Absolutely! But that's the whole point in fleet play. You shouldn't concerned so much about losing ships as much as winning engagements (by making the opponent lose more ships than you do).
Of course, scouts would also need to be properly implemented, which begs the question: how can you easily tell an AI-run scout in your fleet that you want EW lended to certain ships, use 'x' number of channels to break lock-ons of drones targetted on certain ships, etc.?
I think that you will find that seeking weapons tend to be a LOT more devastating in fleet play. It's easy enough for one ship to peel off when targetted, but wheeling an entire fleet around is another story...
Assigning ships to formation spots probably wouldn't be that hard actually. As the 'mission start up' screen pops up, you would take a minute to choose your formation (eschelon, line abreast, or whatever). Each formation would assign a number to given spots (the command ship being in the #1 spot, in the rear of the formation for example), and other ships would be assigned a spot in the formation. As formation spots become empty, the next ship down fills that spot (i.e. if you lose your #4 ship in a 9 ship formation, ship #5 goes to 4, ship #6 goes to 5, etc.). Changing ship assignments during a battle would be distracting (i.e. go to fleet interface, click on ship #4 and reassign it to #7 or whatever), which incidentally simulates the chaos of such occurences... The SFC fleet interface already does this to a degree, but this would need to be upgraded for the nine ship fleets.
Regardless, I think it would be best to limit battles to 18 ships (9 per side), barring special cases, which incidentally are the current SFC OP limits. i.e. six players, 3 ships each, minus the larger formation options.
I'd also envision in that interface an option to 'lock' the point of a given formation on the command ship of the opposing formation, so that a formation would wheel to face the enemy, keeping the rear of the formation away from the enemy. I'd also envision options to break formation and scatter, attack at will, etc., should such be required. If you are hopelessly outnumbered, breaking up and running in multiple directions might at least save some ships in your fleet.
In the interest of those prefering 'loner' play, you could have the mission selection screen offer different options for fleets and skirmishers, i.e. loners get a lot of 'convoy raid' and similar missions, while fleets tend to draw starbase assaults and such. And I'd think that fleet missions should affect hex DV's more than skirmisher missions would. And you could introduce an additional mission selection group for 3 ship fleets, so that they aren't always drawing larger fleets (unless they so choose).
I'd also envision a starbase assault mission, which has live players on each side, assigning additional AI ships (equal to the starbase) to the attacker's fleet, which would be incorporated into the attacker's fleet in some manner. This would reflect the F&E command point rule (the fleet admiral has assigned additional assets to take out the base).
The main question in all this is: can the 'data packets' that SFC sends back and forth handle such large fleets, or will online play bog down? Also, I'd think that in the interest of actually allowing players to run their fleet, that fleet engagements would run at lower game speeds (example: speed 8-9 for single ship, speed 7-8 for three ship fleets, speed 5-6 for 9 ship fleets). That way you can actually direct your fleet somewhat rather than simply hoping the AI does what you want.
Some 'hey fleet target this ship and fire', 'concentrate on fleet point defense', 'everybody go evasive', etc. buttons would also be nice...
Three way fleet engagements are bad, and probably shouldn't be allowed, in the interest of game stability. 36 ships in a single engagement would be interesting to watch but no fun to be in the middle of, especially if three opposing fleets simultaneously decide your fleet has to go...
Hmmm, I wonder if you could tweak the method of mission assignment so those desiring to patrol a single hex all the time could ask for missions without having to leave the hex? Or for those desiring the fun of running a starbase, allowing them to do so (click on mission interface, and you get to choose between sabotage, cargo inpection, merchant pirate soldier spy, etc. missions.).
Also, you could introduce two new variables into the game for fleets: Special Weapon limits and Special ship limits. Hellbores, PPD's, etc. would have a number of points assigned to them, and your fleet couldn't exceed this point limit (i.e. the interface would tell you "this ship exceeds current weapon limits" and you'd have to buy another instead). Special ships could also be similarly limited, such as drone frigates (i.e. no more than 3 DF's in a 9 ship fleet). And the limits could scale to the size of the fleet. Example: you earn 10 'weapon points' for every ship in the fleet. PPD's cost 11 weapon points each, so a 9 ship fleet can have 8 PPD's (88 weapon points, 90 allowed), while a 5 ship fleet can only have 4 PPD's... You could also write some exception into the code, so that you can always take one ship that would otherwise exceed the limits, as long as no other ship in the fleet can pack special weapons, i.e. a 4 PPD DN is worth 44 'weapon points', so if it is flown in a four ship fleet, it would normally exceed weapon limits (40). But, since it would be the only PPD-armed ship in said smaller fleet, it is allowed.