I cruised to 1k with Aeon, and the overarching feeling I get is that effort per reward does not feel good relative to other factions. Take this with a grain of salt, as I'm sure part of it comes down to my APM and situational awareness. That said, there are a few particular aspects that I feel are not so much 'high skill - high reward', but rather 'maximum try hard for average gains'
Issue: The 2 gun upgrades cost an extra 200M & 6,000E. For this, you get 5 meters range, and that's it (no change to speed). The extra range is nice when you learn to manage the sweet spot (I consider that to be a good instance of 'skill = reward'), but it doesn't quite feel like '200 mass & 6k energy' worthwhile.
Suggestion: I'm sure that buffing the guns would cause a riot, so I suggest reducing the costs just a bit.
In my dreams: Single nano-repair on the right arm. This would allow for a 'brick wall' defender build; engineering, nano, shield. Plus it makes sense thematically, given that Aeon originally worshiped the Seraphim and tried to emulate their tech.
Double Chrono - I don't know what this would look like, but cost should be similar to Seraphim's AoE upgrade; a T3 resource investment.
Issue: If you are caught off-guard for just a second, your T1 army is dead without inflicting corresponding damage. I feel this is a prime example of 'not high skill, but maximum effort required at all times'.
Suggestion: Increase movement speed a bit. If you are rushed and ~5 seconds delayed responding, Aurora should be able to moderately retreat, saving at least some of the army.
Issue: Perfection or death. As I've started playing higher-level games, I've found that nobody neglects mobile AA. A single T1 anti-air can defend against 2-3 Mercy. When you compare the relative costs, that seems incredibly silly. At that point, a full Tac Missile base is a better investment.
Suggestion: Increase Mercy's hitpoints such that it can withstand at least a few volleys of T1 anti-air. A single T2 AA can destroy it in 1 pass, sure. But T1 AA should require several shots per Mercy to make the unit viable.
Issue: The GC trades all utility functions for hitpoints and the suction claws. At the T4 stage where groups of 10+ Brick & Percy are common, hitpoints quickly amounts to very little (doubly so when the enemy can casually throw away a group of Strats & Gunships on the GC).
Suggestion: Consider the variety of utility that other T4's get; Stealth, Torpedo, Range, Anti-Air, Shield, Omni-directional firing. GC has the suction claw, that's it. I therefore suggest (if at all possible) buffing the claws. Right now they are simply unreliable and slow. A faster recharge between grabs and the ability to reliably use both claws at the same time would help a lot, I feel.
In my dreams: Put the head on a swivel so it can attack while retreating and/or flanked.
Issue: Remains the game's most expensive bomb. Great when you already have air control, but that's true of all T4. The issue I've found with Czar is that it lacks mobility. Other T4 air can easily 'hit and run'. Czar is the only unit that must be effectively stationary to attack.
Suggestion: To address this, I suggest buffing the Czar's 'pickup speed'. It's 0-60, if you will, reducing the time needed to go from 'idle' to 'zooming across the map'. I see no reason why Czar should not have a 'hit and run' option like the other T4 Air.
That's all I got, thank you if you actually made it this far. Note- I have not played enough Navy to offer any critique of Aeon's arsenal there.