HW1 was counting ships by unit per class - so much per fighter, so much per corvettes etc.
HWC was counting ships by crew - so much supports unit per one type of ship, so much per another type.
HW2 was counting ships by squadron numbers - so much units in squadrons, so much squadrons are allowed per class.
Squad system wasn't used only in HW2 - it was also seen in Haegemonia and WH40K:Dawn of War. Last one was also Relic's doing, and I liked it more then StarCraft, for example. :P
One of the things I liked there was squad improvements: like space marine squad could be converted to tank busters, shootah boyz, heavy unit killers and so on. Along this, squads could have a hero: create a mighty unit - something WarCraft3 influnced - and then just add it to the squad as an addition. Or make a sergeant. This way, quite weak squad of imperial guardsmen, for example, could be turned into something you need to be aware of.
As we see, we can count ships in HW in three ways - it's quite interesting how HW series inside itself has turned into genre experimental lab - by unit, by SU, by squadrons. And me find advantages in all three ways of counting ships (like sheep to the rhytm of the war drums...) - all three can be combined together making player head explode. Squadrons allows you control less while having the same numbers. Counting per class can limit unit number max count, and counting per unit would create variations of strategies for player (of course, then class limits alltogether should be a lot bigger then SU limit).
What am I aiming to? Well, like in big 4x TBS strategies, there should be squad constructor. Can be opened in-game, but better to construct your dream squad - with basic, advanced tactics, with formation selection, with units selected and their behaviour, random icon, before the game. Of course, if you setup squadrons with too complicated conditions - too expensive, too research-advanced, too much SU - then you might not get in-game. So, you will have to balance it yourself. From game developers it would require only to balance unit themselves, set price and SU for single units, mb, basic squads like in HW2. Of course, squadron prices won't be so round as they are now (350-500-550 etc).
Like in real life - you have basic squad of 8 men (NATO standard), but it can be enforced by machinegunner, grenade guy etc, increased its number to 12 or more - depending on the tasks to execute.
So, you would be able, to create squads of interceptors, strengthtened with defence fighters. Or Heavy Resolution squad of minelayer corvette, defenders and defence fighter to protect resource spot. Of course, you need to have control of separate units, but this, probably, could be done with solution of fleet tactics - you would be able to set single unit actions, but it won't excluded from the squadron.
Capital ship combination with strike craft would do nicely: ICF + Flak, or Missile Destroyer + bomber squadrons and support units of support frigate, repair corvette/worker, defence field frigate, defence fighter etc
Talking of support units - their behaviour needs to have separate triggers so they don't try to kill everyone instead of repairing or protecting units by force shield - less of micromanagement. They can be added in DoW way, actially - squad + support unit: not attacking with everyone, not guarding, not following, but supporting, doing their staff depending on specialization. And if this support unit is set up as part of squadron, it would be easier to understand what's going on the battlefield - to see not all the ships, but tactical groups.
Of course, need to think of recursive squadroning - "dawg, I herd you like squadrons, so I put a squadron in your squadron so you can...". Yeah, because we can... Nah, no squadrons in squadron :D.
It reminds me of Impossible Creature, actually - another one Relic's project, where you could create animal mutants with flaws and advantages of each animal part. Create you perfect squadron, meh!
And as we started talk of "parts" ("to become selves"), capital ships could be constructed in R.E.A.R.M. or Complex or... I dunno... Endless Space way - with setting up armor, ammo etc. Of course, it would require balancing of capital ship class and then with strike crafts... Well, it's much more complex then squadron creation that is just cumulative combing of existing ships.
Well, after all player will get his dream squadron capable of attacking and defending itself, instead of getting single fighter that would die in a seconds alone.