Aeson had an excellent post in response to the "Optimal doctrine selection" topic. In that, I'd like to "think out loud" regarding the "I find ammunition doctrines to be a bit too coarse for me to feel entirely comfortable specializing the ammunition loadouts..." issue.
One potential way could be perhaps so that while we should keep the Doctrine's shell selection...
...the ship designer could get the same choices for the armament section:
The player then, if wishes, would have the ability to basically override the doctrine tab for the given class of ship. These numbers would still represent percentages. Say, the player would be able to change these settings - either restructure the loadout or just switch directly to "automatic" doctrine - within a refit of one month of duration.