What if a Military personal resource was introduced
a fighter would need only 1 pilot where a massive battleship would need over 1000 people to make it run properly
This is, unfortunately, difficult to justify when you can have a single transport ship carrying 1 billion soldiers, and it costs less than anything else in your navy (this is under the GCII model, mind you). If you can spare 500 million people for an army in just one basic transport module, you shouldn't have any problem whatsoever finding a few thousand people to serve in the navy.
Beyond that, judging by historical military levels, human nations can sustain ~5-10% of their adult population as members of the military during peacetime, and upwards of 40% during wartime. If we're looking at a multi-planet empire and considering only the requirements of the space navy, well, I think you're well within your <10% limit of peacetime military personnel even if you have hundreds of millions of people in the navy (which, judging from the crew requirements listed in GCII's intelligence report under the 'details' menu for ships, would mean that you have tens of thousands, or even hundreds of thousands, of ships).
this could also have alot of differnt mechanics in it if your main fleet is destoryed you not only loose the fleet but 100k of your soldiers just died you people are not happy with your millitary incompitance
The whole "100K soldiers died causes huge morale hit" thing is terrible when the invasion of planets requires you to bring troops in quantities similar to the total population of the planet being invaded, since the resultant casualties tend to number in the billions (or at least hundreds of millions) even on the winning side; conversely, it should hardly matter for fleet engagements that don't involve troop transports or colony ships, because individual ships rarely have crews much over a couple thousand, according to the intelligence report screen under unit details.
I could see Carriers introduced as a way to extend the operating range of little ships - instead of having to have your 10 sectors worth of life support units on every ship, you could instead have a single ship with lots of life support modules that also has 'hangar bays' which would allow your fleet to ignore the life support limits (or average the carrier and supported ships life support range in some fashion) on X of your ships below size Y (possibly up to X 'ship points', where Tiny costs A ship points, Small costs B ship points, etc, potentially with a maximum size per hangar bay/cargo module/whatever you want to call it), as well as allowing you to ignore the speed limits for those ships that fit into the hangar (which would also allow a similar module that doesn't allow you to ignore the speed limit of the little ships, which would fall into a 'fleet tender' style role). Or they could introduce a more complicated support module where each ship can carry so many supplies or so much fuel, and various types of hangar bays or other support modules allow you to extend the fleet range.
I tend to disagree with the premise that smaller ships should be deadlier, depending on implementation - I absolutely do not want to see a return to the module size scaling of GCII, not when there was no reasonable explanation for it. If weapon A does X damage no matter what ship it's on, and the game doesn't model ammunition restrictions in any way, there's absolutely no reason for weapon A to take up more space on larger hulls than on smaller hulls. Defenses I'm a bit more okay with size scaling - it makes sense that the armor plating on a battleship takes more space than the armor plating on a fighter, and it makes sense that it might take larger shield generators or more chaff dispensers to adequately protect a cruiser than a corvette; same goes for life support and engines. But weapons? My Death Ray takes less space on a fighter than on a Battleship despite there being no apparent difference due to the ship type mounting it? If my fighter Death Rays were weaker than my Battleship Death Rays, I could understand it, but not when they're functionally identical. I would tend to say that smaller ships should be more focused on firepower than survivability, and that the game mechanics should allow you to swarm big ships which aren't designed to deal with little ships in such a way as to give the little ships an advantage (overkill on big guns with long cooldowns, targeting difficulties of some kind, blind spots in fields of fire, something), but at the cost of making the little ships relatively fragile. GCII gave weapons perfect accuracy, and additionally gave big ships the defense and health advantage over swarms of little ships, and when it started allowing ships to target multiple units in any given round it took away the overkill factor which helped swarms survive.
We could have certain ship modules or utility that require a larger chassis to carry. New high-tech SuperRailCannon requires to be installed on a battlecruiser, for example? Or some special weapons that change the battlefield (AoE weapons, maybe? Less direct damage tho) require bigger ships.
I think it's a very good idea to have some weapons of such a size that they cannot be mounted on smaller vessels, as long as these weapons aren't made impractical due to it being better to mount 5 Fighter Laser Cannons in the place of 1 Cruiser Hypervelocity Gun or some such situation (I wouldn't mind that there might be scenarios in which that might be the better option, but I would want them to be special case scenarios - i.e. when creating an Anti-Fighter Cruiser instead of your standard Heavy Cruiser).