(Hi - just super quick; I'm pretty sure the majority of what you're talking about AI-wise is fixed in RC15.)
Thanks for looking into it; I updated to RC15, using the same RC12-generated saved game (not sure if that matters), but still see a lot of AI issues -- not necessarily the same ones as before though:
1. The Medusas, when told to eliminate a target, will happily expose their rear (unprotected) engines to other ships to get blasted to smithereens. Not sure if this has to do with the Medusa having omni shields by default but having the front conversion hullmod; not sure if the AI takes this into account. Granted, elimination command does mean "eliminate at all cost" but it should not mean "eliminate at unnecessary cost", when the Medusas will either maneuver or teleport from previously safe positions to positions where they expose their vulnerable parts to other ships. This also includes taking on a lone Radiant when a lone Medusa (other ships weren't there yet) at high flux will maneuver/teleport to directly in the path of the Radiant's front hardpoints to get obliterated by its autopulse lasers. In fact generally speaking Medusas will happily engage Radiants but hesitate to engage frigates/destroyers, but not sure if this is just confirmation bias.
2. The Medusas still seem to be more "scared" of enemy ships than the Drovers. I still see Medusas disengaging from easy kills when at low/zero flux, while nearby Drovers are still charging full speed ahead. Again, all ships (Medusas and Drovers) have aggressive officers, while Drovers only have Salamanders and Light Machine Guns as weapons, so there's no reason for Drovers to be more willing to engage ships than Medusas.
3. I thought maybe there might be something to do with the Eliminate command, but even with Engage, Medusas will back off (in fact back off even more i.e. farther away), while Drovers still run in.
4. Even when told to Eliminate, i.e. to save a Drover under fire, Medusa will come close and then back off, letting the Drover die. Medusa was at zero flux.
5. Generally speaking, there's no reason for Drover AI to decide to get closer to enemy ships than Medusa AI, when the Drover only has Salamanders/LMG (and broadsword/spark) while the Medusas have SO and lots of short-range weapons. But I still see this happening very frequently. I thought it may just be due to inertia (for example, Medusas can retreat faster than Drovers, maybe Drovers simply couldn't change direction quickly enough, etc.), but I'm seeing Medusas running away while at low/zero flux while Drovers will just stay in melee range of enemy ships.
6. Funny thing is, enemy Scintillas (destroyer carriers) have no problems running away from me, i.e. I can see them starting to back off long before I get into weapon range, and they have worse speed/maneuverability stats than Drovers, plus actual non-PD weapons. Not sure if there's something wrong still with carrier AI when they only have missiles and PD regarding staying a proper distance away from enemy ships, or something with Medusas (due to SO or whatnot) being unnecessarily hesitant.
On a separate note, I messed around with having a Radiant in my fleet. The Radiant seems to drop its shields and try to armor tank unnecessarily, i.e. at low flux, when in combat. This means its weapons quickly get disabled and it disengages. That's not good AI behavior when it's the tank.
Screenshots:
screenshot002.jpg and screenshot003.jpg -- At the bottom is a lone Lumen. The Medusas to its right were attacking it, then backed off. The Drover kept pressing forward. Maybe the Medusas were leashed by the "Defend" and "Capture" commands, but I doubt it, since they will happily pursue ships much farther away before being leashed. Those commands were set at the beginning of battle and in fact the nav buoy used to be mine before the ships left to pursue other ships. The Drover kept trying to chase the Lumen while the Medusas backed off, when the Medusas were perfectly capable of finishing it off.
screenshot013.jpg -- The Drover at the top went out of position, then got in trouble. So I ordered the Medusas to "Eliminate" the Fulgent that's attacking it. The highlighted Medusa closed in (to around where the missile above it is), then backed off without firing. Zero flux. Drover died.
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