Step in the right direction, but...
I'm not sure the fleet cap (issue #3) makes all that much sense to be honest. Wiz ourtight says there is still no limit to the size of the battle. So instead of 1 doomstack, now you have three seperate fleets, all set to follow one another ... but still working as a doomstack (and now with more micromanagement!).
Issue #1 and the solution of "Force Disparity Combat Bonus" is stupid if you ask me. Especially combined with the command limit. What happens when I decide to split my 3-fleet doomstack into a 6-fleet doomstack - how do these bonuses stack (hopefully it just takes all combatant into account).
In any case, this is a band-aid patch if I ever I saw one. "Hey, bigger fleets are too strong, let's just make a magical buff to smaller fleets to compensate!" I don't buy it. Sure, it will help even the playing field, but it's painfully artificial.
Issue #2 with the retreat mechanics looks great, makes sense, and will have a nice impact. My only worry though is that fleet battles will snowball more quickly. If ships start vanishing at 50% damage your force strength will drop very quickly. But in that case you were going to lose the battle anyway. Realistically, if you get into an engagement you won't win, your best option is still to FTL jump away the entire fleet as soon as you can to minimize damage, get your fleet back quickly, and repaired more quickly. So really, nothing has changed.
The problem with Doomstacks, IMHO, that developers don't seem to acknowledge is that doomstacks are a symptom of how strategic warfare is structured in most 4X games. All of the typical well-intended solutions (fleet limits, emergency retreating, yadda yadda) are all tactical-level band-aids that don't change the underlying strategic-level incentives.
The basic question to ask is this: what incentive is there for the player to have multiple fleets?
In most 4X games, there are NO incentives at a strategic level. Hyperlanes and fixed defenses protect your empire and don't require you to spread around multiple smaller fleets for defense. For offense, you want your whole fleet doomstacked to quickly overcome those same chokepoints. There are no incentives for raiding fleets to blockade or disrupt supply lines (because there are no supply lines). Fleets all move at the same (or close enough speed) so there is no real gameplay in strategic position + manuever. There are no stealth or detection mechanics in most games that could, for example, make smaller fleets harder to detect and therefore able to be more effective at raiding back lines. Games rarely have mechanisms for pinning hostile forces and making it risky to have your eggs in one basket. Ironically, Stellaris got rid of their battleship modules that did exactly this. That was a big WTF moment for me.
In short, 4X games - especially 4X space games - do an absolutely miserable job creating an interesting strategic-level system for warfare. And until dev's realize this and actually make some interesting mechanics that create INCENTIVES for something other than doomstacks, we're just going to be reapplying the same old band-aids over and over.