So you finally went through and officially labelled it 2.0?
Many people have proposed solutions to Doomstacks. Some have been simple, others complex, but what most of them have missed (and the reason we have taken so long to address this) is that there is no one solution. It is a complex problem with multiple causes and problems, and the only way to begin to address it is to tackle those problems individually.
I think you guys had the one-up over us there. I don't think any member of the community would have dared to suggest a multi-step solution concept on that scale

But it's nice to see a few community suggestions mixed into your solution.
The Force Disparity Combat Bonus is applied when a smaller force is engaged with a larger one in battle ('force' being every ship engaged on one side of a battle, regardless of how many fleets and empires are involved on each side), and gives a bonus to the firing speed of all ships belonging to the smaller force.
This is a very interesting move. It's obviously going to draw complains from people aka 'mah realism' (I mean 'they have more freedom in maneuvering' is a half-hearted reasoning.), but it definitely sounds like something that could work out.
Rather than always fight to the death, ships can now flee battle and survive to fight another day. In combat, any ship that takes hull damage while already below 50% health will have a chance to disengage from battle
That's not quite Fleet Morale, but it's close enough.
Command Limit is a limit on how large any one individual fleet in your empire can be (right now it's a hard-cap, though we might change it into a soft-cap)
Please do change it into a soft-cap. If I get stuck with 27 Fleet limit, I will go mad over not being able to have a clean number like 30 ships.
We believe that these changes, together with many of the other changes we are making (Starbases, FTL rework, etc al) will naturally change the way wars are fought away from Doomstack primacy. Certainly, there will still be wars decided by large-scale engagements of both sides' navies, and certainly it will sometimes be advantageous to keep all of your fleets in one place. But this should no longer be the only way to play, and there should be many new tactical and strategic opportunities available to players in how they use their navies.
As much as this sounds intriguing, I'm slightly worried about the AI's capability of recognizing, deciding on, and deploying these kind of warfare tactics...
I mean, we still, at times, see the AI struggling to do anything because two fleets keep 'following' each other...
requiring a fiddly excercise of swapping reactors for shields/armor and vice versa
Thanks for removing that bit.
to balance between weapons, shields and Aux utilities.
On that point, did you ever consider allowing ship modules that actually differ? Right now, all you can do is chose the size of your guns, or replace 2 guns with a torpedo tube or a hangar (simplified).
I would really love to be able to chose modules that have less guns, but more defenses, or vice versa. I want heavily armored cruisers with a couple weak weapons glued to armor plates on the front, and fragile gunslinging sniper battleships in the back.
I know that would require even more balance testing (and probably ship modelling, since you would probably object to having multiple ship modules with the same model (abeit I personally don't really care for the ship's looks, over gameplay)) and won't come in 2.0 either way, but might be put (or already present) on your TODO list.
so we created a formula for mapping armor to damage reduction that pretty much nobody understands
Including the devs?
the rather ill-suited Energy Torpedoes that aren't Torpedoes at all but just a regular energy weapon, resulting in even more confusion and diffusion
Standards and consistency are for the weak.
It also means that empires that want to invest heavily in the power of missiles will need to use designs and ship classes that can pack torpedo slots, instead of simply putting missiles on everything that would normally mount a different weapon
Which loops back to my above mention about ship modules. I would hope you will amend modules some for this change, to actually allow making dedicated missile-only ships. Because currently, you would have to put a mix of missiles and other weaponry.
As well, how does this affect starting weapons and the general early-game?