here's how I would solve this then... And I did it only by modifying config settings... But again, my solutions are very stupid, and this could easily backfire in some way...
A - I've changed how you gain bonus experience. In vanilla game you gain bonus experience for retraining, mentoring and recruiting new officers (promoting). I've made it so that retraining doesn't give bonus experience. But made it so that giving elite points does. Now, why? This is cause I wanted the game to work in a way in which you want to rotate officers, rather than having an elite you hold onto for the rest of the game. And having a system where retraining is more encouraged than training may allow that.
B - I've made mercenary officers far more common, and gave them a shorter timer before they no longer work for you. With mercenary officers being ridiculously common, you may more easily assemble a proper fleet of high level officers that have specific stats you need. And in fact you may be allowed to have a fleet of high level officers way sooner, by substituting long-term officers with mercenary ones. Who are also going to rotate quickly, allowing you to rapidly change strategies depending on what kind of officers you have at the moment. With only a select few being permanent. At least until mid, late game where you have a large base of normal officers.
With this system however you are encouraged to fire and recruit new officers often. Because as I said, training officers gives you bonus experience for giving them elite skills, as well as mentoring. So you are no longer encouraged to just endlessly retrain the same officers over and over in hopes of somehow fitting them into rapid playstyle changes.
You are going to have significantly more bonus experience due to the fact that you will be recruiting a lot of mercenary officers (but will also have them leave you way more quickly, cause I nerfed their timer from 730 days to 180. So stacking large amounts of mercenary officers may still prove difficult). And if you choose to train and fire officers constantly, you will have an easy way to rapidly farm bonus experience... Which, I know... Sounds stupid. I need to know how this works at the highest possible level where experience values are so ridiculously high, only the strongest fleets give you anything. And at that point why even bother playing the game if all enemies are trivial?