I can get to the final Radiant and Apexes destroying all the rest. Unfortunately I can't win the fight despite repeated attempts and due to overconfidence I've locked myself into it, saving 1 second before the fight.
No spare story point? Clean disengage option? Can always just turn on dev mode and teleport out (Ctrl left click).
Also the gameplay is totally unenjoyable, it takes the normal herding cats experience of high level Starsector and turns it up to 11. I run out of CP trying to make them not chase frigates. I think the fleet would win if I could set the ship to not do so.
Eagles really want to be in a mixed fleet. And technically don't necessarily need to be herdered that much, I think.
As a quick test, I took the fleet I was using testing 6 Gryphons and swapped them out 1 for 1 for Eagles and did a single quick run (also tuned Officers to match since Missile Spec isn't quite so handy). And used the exact same orders. Afflictors to grab far objectives, grab closer with Radiant and cruiser, issue defend order on Onslaught. Order an Afflictor to escort Radiant, cancel objective order, and let the defend order on the Onslaught keep the fleet together, and basically ignore fleet orders after that.
Eagles were 3 HVD, 2 Graviton, 1 Ion, 3 LR PD, 2 Burst PD, 2 Reapers, Missile Autoloader, 26 vents, 17 Caps, s-mod Hardened Shields + ITU. eCE, eFM, eOE, GI, TA officers. So a long range shield damage ship designed to keep enemies at bay. Compared to spam Gryphon, I got about the same final result, although the player piloted Radiant actually saw a lot more action rather than the enemy kind of evaporating from the missile storm of Gryphons. However, I've had cases where a bad Nova engage saw a Gryphon pop, and something similar happened with the Eagles. However, they held the enemy back enough to give the Radiant and Onslaught a place to ditch flux, which is all I really needed.
I suppose if I were actually paying attention more I probably could have saved the Eagle with a well timed Afflictor distraction, but shrug. Same thing happens with Gryphons.
Keep in mind, the fleet wide skills were Coordinated Manuevers, Crew Training, Flux Regulation and Cybernetic Augmentation, so these aren't exactly top of the line AI controlled Eagles, but they held well enough.