This really reads like "Space is big therefore tactics don't exist, everyone lines up and then blazes at each other because there's no other alternative."
I don't buy it. Are ships positioning themselves that far apart in game? No. Do most weapons have that much range? No, except for spinal mounts and artillery. Furthermore, this theoretical massive engagement range where everything can shoot everything is something that's just taken for granted, but not necessarily true. Ever heard of Aurora 4x? It's a game of sorts, often called the Dwarf Fortress of 4X games. It really slams some things into the ground regarding assumptions, one of my favourite being about engagement ranges and sensors. Never assume that everything is meaningfully visible to everyone in space. We can see heaps of things in the solar system from earth at huge ranges, but that's because we have huge arrays of sensors. A ship just has its own and the sensors of the ships around it. If say, a targeting sensor can see really far, it might not have the resolution to actually lock onto a small target, unless the sensor itself is big, etc. Nothing of a given size can do everything. I know Stellaris isn't Aurora 4X, but the situation you describe isn't Stellaris either.
A spaceship is about as subtle as a flare on a moonless night. You could see it coming lightyears away if there is no FTL involved. That's for several reasons, its thrusters are an instant giveaway, that's the equivalent of detonating nukes behind your ship. The next thing are its shields, they project energy and light it up like a Christmas tree. If it doesn't have shields and no active thrusters it still radiates in the infrared, and that is something unavoidable, ships are so much hotter than the space around them that it would get picked easily without the need for massive sensor installations. The only reason we need them is to look at other stars or even galaxies, and the Hubble space telescope is much better at it anyway because there's no atmosphere in the way, the same would be true for spaceships. In a setting as Stellaris, I can't conceive any way in which a spaceship could avoid detection unless it's hiding behind something else or at some point cloaking is invented.
I recommend watching the episode about space warfare by Isaac Arthur, he goes in depth why you can't hide in space.
Where does fleet cap capacity come from? Part of it comes from population. If your population is occupied, how can it give you that fleet cap? It's logical.
Regarding the empire wide happiness penalty, you're talking about something akin to war exhaustion, that might be something good, however I'm far more interested in harsher per-planet based penalties, as that means that specific planets can be targeted which makes for interesting strategy rather than occupying some useless fringe worlds and nerfing the enemy empire-wide. I think the idea of resource storage being accessible (linked in the summary under "Planets as high value targets" ) is a good one because it makes invasions really worthwhile and concerning for the enemy. I'm not entirely sure about making bombardment give huge penalties because it makes planetary invasions even more irrelevant than they already are.
I'm not really a big fan of the fleet cap in general, I feel it should depend on your economy how many ships you can support, not some arbitrary limit. I also think the economy of HoI would be better suited to Stellaris than what we currently have.
Maybe I didn't explain it very well, there should be an empire wide penalty for not protecting your planets, for example a happiness penalty that doesn't instantly go away when the bombardment stops, but an even higher penalty for actually losing the planet to an invasion, but it should start small and rise the longer the planet is being bombarded or occupied. I would also give a diplomatic penalty for bombarding planets longer than necessary, but that's just me. The planet itself gets a modifier as well, something like "recently bombarded" and "recently occupied" that ticks up the longer the planet is under bombardment or occupation, which reduces productivity by a significant margin and gives the amount by which it is reduced to the occupier, here I would actually let the bombardment modifier be worse than the occupation one. If the siege gets lifted the bombardment modifier starts to slowly tick down, if the bombarding fleet was driven away you could apply a moderate happiness bonus for a short while. Occupied planets lose less productivity, but their resource output goes to the occupier instead, this would give a large incentive to both invade valuable planets and protect them, since not only are you getting deprived of the resources, but your opponent gets them instead. Taking the planet back gives a moderate happiness bonus again.
That aside, what do you think of my take on system wide auras?
System wide auras are fine by me, I think anything that makes defensive stations better in such a way that it doesn't encourage doomstacks is a good idea. That's why I think that defensive stations should have a much higher range, they are so far apart from each other, that going at them one by one with a doomstack is less efficient than taking them out with multiple smaller fleets, especially if sublight speed depends on fleet size.
Several people suggested a more RTS-style control. Maybe allowing control of fleets even in battle would solve lots of things. If we could retreat in a normal way by just turning and flying away while being shot at, that would make for interesteding strategic decisions. If we could kite and stay at range, weapon range and speed would be a lot more interesting and make for much more dynamic battles. Being able to kite / run away would also encourage spliting of fleets. Flanking would become a thing even without flanking bonuses just to cut the retreating path.
This would be a step in the right direction, but unlikely to happen I think. There should at least be an option to disengage from a fight to retreat towards your defenses, it makes no sense to me, that you automatically engage the fleet as soon as it is in range.
We Could have AoE weapons, maybe even some that have to be aimed by the player itself. That would devinitely encourage splitting and it would allow for a technically weaker fleet to pose a thread to a big stack if the big stack owner doesnt pay attention.
That's a terrible idea without tactical combat, the result would be that you just split up your fleets into multiple smaller ones but still move them together, you'd micro them a bit so they can't all be damaged by a single shot and that's it. The extreme version would be that you control each individual ship so AoE doesn't affect you.
Edit: I also think having small raiding fleets is severely underrated right now since people just don't seem to get the instant gratification of seeing their warscore increase by killing enemy mining stations, yet it can win you a war by destroying the enemies economy. If we had some kind of espionage if may be possible to see enemy mineral/EC income and therefore therefore it would be more obvious what raiding fleets actually do. However, I think with time passing people will realize raiding fleets are actually really good escpecially because even very small ones can deny a lot of income to the enemy.
Actually, since mining stations contribute too little to your economy and cost less than a corvette they aren't worth the effort. They would need to be more valuable and more time consuming to replace. It would need a rework of the economy, but I think it would do the most to discourage doomstacks.