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Firstly, I want to thank you for engaging in this discussion, as it seems, on a genuine basis, and for arguing around the points brought forward.
Sorry for the long delay, been a hectic week. But likewise, I think we both see the issue but have a different view on how to solve it. My recent/current campaign has given more clear signs on these issues.

I think the spread and the scale really depend on how we scale the progression and the time it takes to build fleets. I would not worry about "too many fleets," and there should be an option for large investments in the military to have more than enough fleets. For an offensive strategy or scenario, like an offensive war, empires should prepare reserves to handle increased front sizes. In general, a simplified system adapted to Stellaris—similar to how HoI handles units, provinces, combat, and overall military gameplay—would create a much better solution than what we currently have.
Time to build up isn't so much of an issue with the length of the game, drawing that out does mean taking losses is harder to recover so would support more keeping fleets in close groupings to try and avoid them being lost and mitigate losses.

Scale of the war depends on the size of the empires, alliances and so on combined with galaxy size. IT would be easier on larger maps to have it automated as it is a bit of a pain, especially once you get gateways and the L-gates.

Exactly, this is inevitable, as all other changes to the game, even the upcoming pop system, effectively do nothing to the game. A rework of scaling, economy, and military is fundamentally necessary, but that’s not something unreasonable to state, as the game was built like that from the beginning. All changes done while the basics remain the same are wasted work and energy. Nothing will change—we will keep doing nothing but amassing resources to amass fleets to hit each other over the head with. The bigger, the better.
Military and the base systems around that might not need reworking if other things are done. The core issue is the gameplay loop which none of these currently solve. What are you going to spend the resources on? In the end there's limits on what you can do with everything but alloys and research.

My current game while I became a large and the most powerful empire rather early on without waging wars (crusader civic), I did run an issue of food. I know, funny that the most over looked resource was actually an issue. None of the worlds within my reach had much in the way of food, I wasn't able to stack bonuses so much to have just a single agri-world supply most of my empires needs. End result, I bought it out of the ether with the market until I built and staffed a few on backwater breeding worlds.

Now that seems like it really could of been a different path to take on the economic side, instead of looking at HoI I looked to Victoria. What if one of my neighbours worlds was perfect for an agri-world? They could of supplied my needs, but gamewise it's more annoying to do that than just click a button to buy it from *hand waves*

This is a balance problem, but I assume you mean what game goals are there besides amassing fleet power via different means?

That is a good question, but as Stellaris tinkers with so many concepts, like the new Lathe for example, there is enough basis to introduce more interesting game goals like this. As soon as the need for every empire to focus entirely on amassing fleet power is erased, the game could allow for a broader range of objectives. The idea is that when you reach a soft cap for your personal comfort—being safe with a stable and capable military for your current position in the galaxy—you can focus on other game goals besides your military-industrial complex.
Not just that, but currently what do you do with surplus food, minerals, energy, etc? Research and alloys? Research is always being used to improve your empire, alloys of course can be used to build up more fleet power. The others...better to avoid getting that much and have the pops work other jobs where you can get something for that work.

But a cap on how many fleets you can have in a single system doesn't give that safety, unless you are the most powerful military. Which means you've been pumping resources in to the military-technological complex in game. Otherwise there's always someone stronger to come at you. Without the cap you and an ally can focus enough strength to have a chance to win.
In addition, any side feature currently underutilized, like espionage, criminal empires, raiders, spiritualists, etc., could be improved. The impact of the fleet power snowball would be reduced, as a limit on fleet power usefulness would allow other systems to gain more significance without ruining your playthrough by losing one of your massive fleets.
Yeah if more of it had reasons to interact with it would make them more interesting and something else to sink resources in to. My current game is Knights of the Toxic God, and outside of clicking events my empire plays no role what so ever in the course of it. There's events with armies and fleets going off and fighting battles but mine never leave the garrison system. I didn't even need to send my science ships out to explore!
It’s more than just "removing doomstacks"; it’s about reworking the fundamentals of Stellaris so the game doesn’t revolve around the fleet power snowball.

To answer your initial question: we could invest in non-military tech to improve our pops’ lives, invest in megastructures that aren’t focused on fleet power, invest in cultural projects (which would require a cultural system as a metric to compete in), invest in diplomacy to create galactic peace (rather than uniting the galaxy under an empire, which is currently another fleet power check), invest in espionage, invest in trading, and develop a wealth and trading system that impacts other empires. We could also create a meaningful internal politics system with real consequences, and so on.
Yeah it does need the fundamentals reworked, but the military side is the last one that needs to be touched to have that result. The focus needs to be on the other systems to make them worth investing in, to have continued returns on playing with those systems. Why I think looking to Victoria would be a better choice than HoI, managing your empire, your actual trade connections and resources would give us other things to invest in and have our fleets and tech be just part of our build up rather than the end goal.
For me personally, the discussions on how it’s done are numerous and mind-boggling. If I had the say, I would just copy a light version of HoI's supply system. Build supply depots in building slots on planets and stations, and have them provide a supply cap within a certain jump range to systems. Each system gains a certain supply cap based on the depots in range. If too many fleets are stationed within the radius of a supply station, it will run low, and combat penalties will occur. It’s the perfect antidote to doomstacking and adds another layer of strategic planning, both defensively and offensively. Alliance fleets would take up the same supply from your stations, so the usefulness of endless vassals and allies would be limited, which would also solve this issue. Of course, this should not create problems where the AI ignores your fleets and the supply in systems, ruining your offense/defense. It works in HoI, so it should work in Stellaris if done properly.
For me supply for the military isn't the right path, if we need to supply anything it really should be worlds themself. If we can supply all the needs of trillions on an ecumenopolisI should be able to supply the fleet these people are paying for.

This also doesn't solve the issue on the military or the current focus on fleet power. We will still focus on research to boost the strength of our ships but now you just add the extra step of us having to take a slot for a supply building and set up habitats just to put a supply building in it. End result is we now want even more alloys to pay for that and get an extra breeder world.

It also doesn't solve doomstacking, I can stack supply depots within my systems to allow me to doomstack while an enemy can't, especially once we get gateways. It also means instant doom in a number of circustances like when fighting a more advanced foe, they can have more powerful ships with the same or even less supply drain which you need to throw more ships at to have a chance.

My view following on with the idea of planets needing to supply their needs, and automatically trading would give more interplay. Suddenly you might want to be on good terms with that empire on your border to gain access to their local supply for your world. If you can't make nice maybe now you want to turn to that criminal mega corp who could set up a smuggling ring? Or maybe you try to cut out the middleman with espionage to set up your own blackmarket trade or make an agreement with pirates to intercept their trade and bring it to you.

If we had more depth to the economy and especially the early take on the strategic resources that gave other benefits than just an upfront cost and upkeep for advanced/special buildings and modules it would give us other things to invest in. The different ethics should want different luxury goods and ammenities. If you had to supply those differences it would also make integrating different cultures harder, so conquering land doesn't always bring about quick returns. Like you said having us improve the lives of our citizens.

As we said about different goals, my current Knights feels like the aim should be about finding the Toxic god. That could of had a lot of direct gameplay with me being sent to investigate sites, talk to the Enclaves and see what other empires knew. Having me take different paths and builds to get that result. Could use stealth ships, direct warfare, diplomacy, covert groups and so on. Megacorps should really be about selling their products across the galaxy, not caring about building up their own borders so much. And so on with other more focused starts. Other "generic" empires can be a lot more free form in their goals, they can still have those that just want to rule the stars. But it means not everything is being solved by getting more fleet power.

So yeah big changes to the core, possibly too much for a rework would need more a rebuild.
 
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I think the RNG is meant to mimic an 'organic' process of random events and happenstances that direct a society down one path but not another. You are experiencing friction because you want a 'teleological' process in which your society progresses according to the ultimate build you have in mind for them. Maybe Stellaris can offer an RTS mode, where all tech trees are available for research. Personally, I'd go the opposite way and base new tech's likelihood to appear on what's already been researched.

Sci-fi reference: 'The Road Not Taken' by Harry Turtledove.
its not wanting a "'teleological' process" its wanting some logic to it. if you are locked in a existential fight for survival with a determined exterminator on one side and a devouring horde on the other and a naturally martial ideology and ruling council why in the hell is researching the fifth repeatable 5% bonus to energy considered more optimal than refined lasers or better ship ftl drives? I agree there should be some level of rng to it but you should also have the option to focus on specific fields that allow you to specialize if the needs be.
 
I agree with your ideas for other types of victories, though I'm not sure how that would interact with the end game crises. Then again, I rarely get to the final crisis. There's usually a point at which I've clearly won, and I usually stop then.
Now that it's been said, I do like the idea of a science or cultural victory for each end game crisis. An equivalent to war exhaustion which you can bump up by diplomacying at them, possibly eventually resulting in various thematic ways to convince them to just, like, cut it out. Two of the crisises are hive minds, one crisis is led by a single individual, and the last has three factions, so there's possible diplomatic, scientific, espionage, or combined approaches to each of these. Hacking or talking down the galactic threat is a staple in a lot of genres.
 
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I would like to have fleets of colossal ships. Playing on Captain difficulty, if Cetanea appears as the fourth crisis, it has a 13.5 million power ship that is immortal, along with other defenses and fleets that individually exceed a million.

There is no enigmatic colossus, and the traditional colossus is more of a curse than a blessing, creating bottlenecks in the only two shipyards it has while the mega shipyard remains idle.

If you focus too much on having massive alloy production, no matter how hard you try, you'll fall behind in repeatable technologies. Even with hundreds of labs, three science nexuses, and vassals researching, nothing is enough to reach those numbers.

That's why it would be great if fleets could scale up as well—whether through colossal battles or simply by adding more weapon and armor slots to the same ships.
 
More patches and further game development naturally leads to more and more complex game mechanics or mechanics with little impact.
That wont change. Many suggestions are more of a downsizing of the game that might as well achieved by the player rolling back to an earlier version of stellaris.
Especially back to 1.9, which can easily be done via steam. Give it a try. We are in the third iteration of stellaris and soon in the 4th. 1.x can be considered a completely different game by now.