My opinions and feeling are based on my experience as a player in game : I play with 500 battle size, and i am often the underdog since my fleets usually consists of cruisers +1 capital carrier + 4-6 frigates not exceeding much over 200 since the slow down in storms and such is very irritating to me ( i just found ou about a x3 time multiplier, it might change my habits ).
In my experience the ship do not often stack behind each other and support armed ships either end up temporarily in the frontline or remain far behind doing very little until they are engaged by ennemy frigate. Those frigates are not deterred by the low dps at all, especially since they can evade most of the slow firing fire. Indeed support weapons having relatively high alpha but very slow refiring make them very often miss their target ( when not beam based ), and lead to even lower than stated long term dps.
My experience might be biaised since i often play frontline cruiser and very often ( have to ) force my other ship to push with me, the lack of aggressivity of ship with steady or without officier is slightly annoying to me, while Agressive Oficiers will suicide themself or abuse of the plasma burn ability and woink themself across the battlefield with disabled engines after hitting a big wreck.
Cruiser level of shielding on a gunship suprised me, especially since its other stats are for now not that far from other gunships.
I somehow missed the assault autocanon costing flux, the flux free version still looks very weak to me compared to a mass driver for exemple. They also suffer from long refiring time and often miss while the multiple 100 damages shots are not that effective against armor, so even when they finally hit it does not do much.
In my experience, a range difference of 100 do not matter, especially since they very rarely hit less than capital size at that range, and capital laught at such tiny damage.
About Atropos, i also noticed both it and the Sabots, and Harpoons have single launcher version with much reduced OP cost, yet they behave very differently : the Sabot launcher no longer have multiple ammo in magazine, but reload time is barely increased, Harpoons's is increased, while the Atropos reload time is extremely increased.
As for Skills : i may not be a good exemple of the playerbase, but i dislike must-have extra abilities in games. Getting small advantage, or extras that matters in a few specifics case is great, getting abilities that completely change the mechanics of science based games is just irritating : either the game is balanced without them and you stomp everything once you get them, or it is and you struggle without them.
Losing a few ships to End Games challenges in a desperate gamble looks fine to me, having to get and rely on abilities to survive againt them isn't, especially if getting them make standart fleets and challenges a walk in the park.
The Plasma Burn ability make the ship "jump forward" a short distance at extremely high speed, the issue is that the AI will use it very often ( whenever it is available i guess ? ), and sometime it will use it and propel the ship against a big ennemy ship, a wreck or a battlestation, disabling the engines of the ship, and letting it go spinning accross the battlefield at 200-300 speed. By the time the engine get repaired and the ship's standart max speed is enforced, the ship crashed in the middle of the ennemy formation or is on the other side of the battle map. Odysseus Battlecruisers are extremely prone to this.
Replacing those abilities that the AI use to suicide themself would be welcome. Yes it is a Vanilla thing, but since AO touches abilities...
edit You already did that ! I didn't touch the Odysseus recently... don't know if other ship still have that terrible ability *
edit 2 : Shrike hight tech destroyer do have that ability
As for the Black hole, it is immersion breaking, and i can very easily see invasion or defensive fleets sometime getting stuck in there too ( i haven't yet, i don't go there often ). Would it be possible to add some kind of buoys with repellant effects arround it ( faking red giants... ) ?