Cybran were supposed to be about stealth, mobility, viciousness, and adaptability/multipurpose. It's why so many Cybran units have torpedoes or the t1/t3 anti-air can shoot the ground. Their original name was "Recyclers," where recycling is just another word for reclaiming. Zero sentimentality, just totally practical, often inspired by bugs whereas UEF is obviously inspired by modern US military.
Aeon were supposed to be severe, extreme single-minded zealots, fitting in with their "religious fanatic" background. Hence why their units often do exactly 1 thing really really well but are missing basic stuff, like frigates and destroyers not having anti-air. Oblivion turrets fire slowly but are devastating. Aeon doesn't worry about overkill.
These lofty ideas don't always show up in a pure way in the game. For example, the Monkeylord has lots of abilities (stealth, speed, torpedoes, anti-air) so it is a good example of an adaptable, bug-like unit. But also it's the cheapest big laser platform out of any faction. So you could consider it to be a "single-minded" single-purpose weapon consistent with the aeon theme.
Similarly, the Megalith has lots of HP compared to the Fatboy. And Bricks are extremely tanky. If we wanted to elevate faction themes over gameplay balance we could "fix" those things but then the game probably becomes unfun. I do think the game designers did a great job of giving personality to each faction.
The Czar really doesn't make sense as an aircraft carrier. If you could have a Czar that is 10k mass cheaper without the carrier abilities (build, store, and repair t1-t3 aircraft) you would almost ALWAYS take the stripped-down version. That's why the Czar should have the factory abilities removed. It's fine if it is a flying air staging but it shouldn't be able to make air units.