While I can't really disagree with you that much, it is interesting how we came from entirely different standpoints.
I actually expected logistics to increase.
Why?
A) Every godforsaken rock in space, of a reasonable size, would be a source for one of those potential base resources. This means that even a system that otherwise comes out empty, is now worth at least something.
B) Let's be generous and assume 8 kinds of handwavium; each of them is also needed in smaller quantities, maybe about 75% of now, while the rest is done by stock materials; and is available half as often.
Now you might be in a situation where you have a large Asteroid field with tons of those stuff, but no large planet or gas giant near, so even if there was a small planetoid available and you got 7 of 8 handwavium at hand, you would need to get that stuff home somehow.
C) Stock materials would be required for the civilian industry as well, and harvesting them from inhabited planets could result in pollution, just simulated by unrest. This would mean to feed the voracious appetite of a 100 year old spacefaring Industry, one would have to place mines on a good dozen planets, and not every single one might contain rare minerals or fossil fuels in large and accessible enough quantities that it would be worth simulating in Aurora.
D) Single Example: Sorium being a bit more rare, mostly on Gas Giants, would allow players to set the mix for their standard fuel.
For a massive peacetime economy, small rations might be enough, maybe 20%; but a Warship would have 50% Sorium fuel to allow for a bit faster acceleration and higher fuel storage while retaining small size.
One could even devise Sorium Boosters that burn the valuable stuff to try and get out of the way of an incoming projectile quickly.
Additionally, you have to keep in mind that Logistics will be somewhat simplified by now having jump routes anymore.
You could complicate matters by making FTL drives cost a certain amount of special fuel, and commercial engines being not as much more effective as the ships are larger, possibly resulting in systems that are a great staging ground for attacks, but too far off to make it economical at the current tech level to ship that fuel home.
Also a possibility
You could even go as far as change the demand for various materials as times change.
EXAMPLE: Player UnLimiTeD recently finished research of Reactive Electric Armor, with a durability 20% higher than Ceramic. However, this new type of armor requires microcapacitors as part of it's structure, which require a different type of handwavium. UnLimiTeD currently does not have enough of that, and doesn't want to buy it from Steve. So he decides to keep using the old armor and order additional amounts of resources for the next Transport convoy to his mining system, hoping that by the time the stuff arrives, he'll still need it.
Theoretically, you could go as far as having those armors be more efficient against various attacks, like an extremely heat resistant ablative armor protecting against Lasers (-25% dmg) but having an overall lower strength.^^Aww, I know you won't. As for stealth, I suppose as a compromise, you could give Living space a thermal signature, even if it's low.
Suggestion #2 (or was it 3?): Could you theoretically change the range calculation a bit? Instead of linear, it could be ^1.5, somewhere on the way to reality, with a higher base range, and factor in things like where the sensor is based.
A military Thermal Sensor Array on a battleship patrol would be able to find you rather easily unless you employ extensive handwavium technology, but a thermal on a Civilian ship that is not constantly monitored, while theoretically having nearly the same range against blatantly obvious threats, would be nearly bling to a small flare now and then, sneaking into position.
On Planets, Active sensors could be hindered by the gravitational field of the planet, and Passive listening posts are more efficient outside Atmosphere.
While this in total might mike stealth harder, it offers interesting decisions, where an ambush on a civilian fleet is possible when a Military fleet would possibly detect one, and covering a system in sensors will be a bit more logistically demanding. It might offer a nice amount of hide&seek where one party raids the other and disappears before the military forces come to hunt them down. As far as that is available in space.
Would a Shield generator be able to hide a thermal signature, but in turn provide an EM signature that is not scanned for on Civs, but might give Military ships a valid target ID on longer than normal ranges?^^