This is...something that has bugged me for a long time. The game works though, this isn't something that requires urgent action! Just a list of issues that I've noticed over time, and I'd hope for them to be lessened or amended in future, when...time allows. I know the schedule is a bit beat up now though.
I hope this doesn't seem complainy/negative or anything - just bringing it up more properly instead of a few pages back Mantis report, or old Discord chat.
1:
Things like the Beam Cannon and Spire Frigate are near useless when stacks are in play. Because they vastly reduce the amount of actually damageable units the enemies have, stacking makes these things not worth using at all. Finding the Schematic Server for Beam Cannons is pretty much an automatic swap hack to get anything reasonable out of it.
2:
Status effects like weapon reload time, or engine slow are much weaker against stacks. I had a case of where I had an entire AI force caught in Inhibiting Tesla attacks, so they had ridiculous reload times, only to lose the top units shortly after, purging the effect and negating it entirely. This is the same with paralysis from Widow Mines (meaning having turrets there to take advantage of it is pointless, because they'll remove the paralysis), and engine stuns from Spider units.
On the other hand, it's possible for one Spider turret to engine stun ridiculous amounts of AI ships in a stack, so they range from either brokenly overpowered to useless. Warbird Starships are far stronger than they seem, because they constantly apply paralysis over and over, meaning they can paralyse, 1600 ships, technically, and don't care too much about stacking.
3:
Stacks can fire immediately after losing a unit, seemingly. I had some Stingrays stacked up, and I put their reload time to 17s instead of 4s. I waited until one fired, then had it killed. The stack immediately fires again, despite having 15s of reload left to go. It was confirmed to be doing damage to the target.
This effectively means slower firing units are vastly more powerful when stacked. Example below.
Let's say you have two groups of 50 Pulsar Tanks. One group of 50 is unstacked, the other is in 5 stacks of 10. Let's also say the players force is vastly more powerful - it has no problem killing these tanks.
The unstacked group fire, doing 50 shots worth of damage. The stacked group fires, doing 5 shots worth of damage, multiplied by 5 because of their stack being high enough to do so, resulting in 25 shots worth of damage.
The players fleet would be able to kill the unstacked group before it can fire again, thus it only did 50 shots of damage. The stacked group however, would lose the top units, then immediately fire again, thus doing another 25 shots worth of damage, going down to 5 stacks of 9. It can then repeat this, doing another 25 shots worth, down to 5 stacks of 8, and so on, so being stacked makes them able to do FAR more damage than they should.
4:
Stacked forces take forever to be decloaked. I had a large group of Space Planes on one of my planets. I had Scout Starships trying to decloak them, but each time a unit of a stack dies, it gets recloaked. There seems to be a small delay before the new stack is targetable (essentially, it's invulnerable to everything), so my Starships have to wait it out, then decloak it again, then wait it out, etc. They didn't seem to be fighting back, so I just ended up leaving several thousand Space Planes cloaked on one of my planets because of how long it was taking to kill them.
5:
This one came from "Weapon Master" on Steam Discussion - stacks are unsatisfying to fight. You don't see the enemy ship count drop in the planet view, so it doesn't feel like you've really done anything.
6:
There can be cases I think where you might have the damage per second output to kill 50 Space Planes a second, but there are only 25 stacks of them! So I can actually only kill 25 at a time. Effectively my damage output is being capped, while the AI is damaging me far more from point 3: above. Even things like the Botnet Golem can be hurt by this, as it fires quite a number of shots per salvo. If the stacking gets to the point where there are less stacks than shots in the salvo, it now starts to do less damage output.