On a related note, I know some people who had an officer in their flagship to give CR and missile ammo, and then they would swap their character in at the start of battle and keep those bonuses without having the the skills which is a closely related cheese strat. I agree with OP that it's an annoying feature of the game.
Guilty as charged when soloing. What else am I going to do with 8 officers who don't have ships. I have no issues with using all options available in a personal challenge fight.
Even in more sensible fleet fights, I don't think that particular situation is too much of an issue, since you're essentially sacrificing an officer for more flagship power, since that officer can't go to a different ship when transferred mid-fight.
I feel like the most effective fix would be somehow restricting officer swapping, like making it take time to gain the benefits of skills after swapping in, or making it impossible to swap officers unless you are in port or something.
Wouldn't help from a late game true power optimization perspective since you can drop a temporary colony in nearly any system.
The only way to avoid this option is to make CR drops instant when swapping officers/support doctrine benefits. Doesn't automated ships do that right now? I don't remember.
Although if you do go the instant CR drop route, I would suggest having it remember what the CR would have been if the Combat Endurance/Crew Training/Support Doctrine/Hull Restoration benefits had not just been changed, and if you swap back while paused, it goes back immediately as well, to avoid penalties for simply rearranging and making a mistake or testing with different officers in the simulator.
This situation leads to fallowing gameplay loop:
Remove all your pilots from all ships.
Let ships recover CR due to Support doctrine +15%
Right before your fleet meet an enemy press pause, study your opponent fleet and remember all the ships.
Press fleet, button.
Assign your pilots to the ships you want to use in the upcoming battle, according to their and yours poweer/skills/DP. (Player have to memorise all those those numbers.)
Go back to space interface start combat
Due to CR slow degradation, all your piloted ships lose about 1% CR before you initiate combat
Due to about 14% CR bonus to all your piloted ships, now you get extra bonuses to :
dmg done;dmg resisted; maneeverability;fighter refit time;autofire accuracy
You could do that, but you have to present the fleet and the rest of the skill selection to really understand if this is actually stronger than simply using the skills as intended, or a different skill pick, like Best of the Best would be stronger.
Support Doctrine is best in the case where you have many ships, significantly over the officer limit. Using Support Doctrine merely to get a +15% CR (as noted a 5% damage/speed/damage reduction buff) is on the weak side for a tier 5 skill point, without the free officer skills and DP reduction. Hull Restoration can do something similar, but also with the fact you don't care about ship losses in combat, just overall victory or defeat.
Given it's trivial to hit the 240 DP limit with all officered ships when heavy on capitals, you'll generally be better off with Best of the Best and the extra story point hullmod if you've gone heavy capital/cruiser, and just grab officer training for level 6 officers who pick up Combat Endurance (which the elite version isn't bad on armor tanking capitals). Or alternatively grabbing a different tier 5 like Hull restoration, or perhaps Automated Ships, rather than doubling down leadership.
A frigate/destroyer focused build is generally going to want Combat Endurance on the officered ships, because the +60 seconds PPT and -25% CR degredation rate is more valuable than many other skill picks even without the +15% CR, at least in hard late game fights which can take awhile, which makes this loop moot.
About the only place I could see this being optimal is for a player who doesn't captain their flagship, and has just the right mix of frigates and cruisers to still benefit from Support Doctrine fully on the frigates, and 9 cheap cruisers or so. Anything else is likely better off with a different skill build or would just be running Combat Endurance anyways on their smaller ships.
In any case, you can already do something similar without Support Doctrine, just with one officer with Combat Endurance and some fully loaded logistics ships. Go to planet in the system you are fighting at, create a colony, lure the fleet you want to fight to the colony, dock at
colony, store all ships but one with officer with Combat Endurance. Repair up to full CR instantly. Swap to next ship, storing the now 100% CR one. Repair up to full CR. Repeat. Pull out all your now 100% CR (degrading quickly) ships, leave the colony and engage the fleet. Even stronger since you can spend the character skill point elsewhere. Once done fighting in the system, abandon the colony.
So modifications to the Support Doctrine skill won't actually fix the issue, if you think it's a problem. As far as the Call Reinforce screen suggestion, all it does is make this particular swapping behavior easier, it's doesn't address the balance considerations.