After using new version of the mod a lot with a few different people, encountered some more issues and have some ideas. But otherwise, have really been enjoying the ability to change ships (and off them) for the purposes of retreating and whatnot, makes having different CR times between players in long battles not that big of deal, because the other player can just hop into another ship while their old one retreats. Also has the fun effect of other players bailing the AI out of normally frustrating circumstances, like when the AI is being too passive or too aggressive, player2 takes control and can put the AI ship back into a favorable position.
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After testing it a lot, I have come to the conclusion that due to the fact playerships are typically under AI control and then selected, sometimes the AI messes with autofire groups turning some off, usually whatever it seems to consider the 'main' weapon group, IE the larges in a capital though sometimes its been things like Pilums, or a battery of medium weapons. To see this, if you watch the AI control the main players ship on autopilot, it toggles off and on autofire whenever it feels like it, on whatever groups the AI has decided it wants to do this with.
I imagine the AI just does this normally for every ship and so, whatever weapon groups are set to autofire at the moment of possession, are what player2 has, and not the autofire settings that were setup in the refit screen. Player2 toggling autofire on/off does not seem to fix this, neither does cycling weapon groups, only way to get around it is by being both fast and lucky, catching the AI before it messes with autofire settings.
I've had the AI turn off whatever weapon group Hephaestus Assault Guns and Storm Needlers were on with many ships as the best example I can give currently, I'm sorry I can't think of any exact vanilla ship/weapon combos that caused this to happen, its been a bit and since then I forgot the exact ships/weapon loadouts from the tests I did, it was fairly common though in normal play.
An issue where fighter wings assigned to ships with hangers in separate modules don't obey player2's target, they still obey attack/regroup, but attack whichever target they want.
There are also these various AI issues that I assume have to do with AI override stuff and other scripting things, where the AI has control over a function even while the ship is in the hands of player2, All SCY Nation ships vent whenever the AI wants, all Knight's Templar ships Priwen Burst whenever the AI wants, Some ships with special systems like a few Seeker ships have their inputs solely given to AI instead of player2 making them impossible to use. I don't know if you have the ability to fix these or not, but just thought I'd point them out incase there was a way, there's quite a few ships with hardpoints or inbuilt weapons in those mods that would be quite fun for coop players, but are effectively unusable because of these issues.
Also a few feature requests.
A target previous button as a option, as cycling through 10+ frigates again to target the one you want if you accidentally go past it takes a bit.
A indicator for whether or not fighters are on Attack/Regroup, in the chaos of big fights it can be easy to forget what setting they are on or see what exactly they are doing at a glance.
A way to see flux/hull levels on player2's ship if possible would be cool too, since the base-game UI that shows that for allied ships can be hidden quite often, at least anything that would help show whether or not player2 is winning their flux battle with a enemy ship if the main player is too busy to mouse over them, as suddenly pausing to check can be disruptive for player2's gameplay flow, especially with the latency of playing over a stream.
A way to possibly control omni-shields, either manual rotation with keys, maybe bindable set facings, or some other form of additional control for omni shields, like locking to the target, as the shield AI likes to get distracted by practically harmless frigates often, instead of real threats.