Kongou failed as Episode 5's flagship because, although she's a skilled combatant, she has about as much tactical acumen as an overripe tomato. Proof? Play the game and see how often she aims for (and massively overkills) the enemy destroyers rather than shooting the really dangerous targets. (Granted, the same is true for virtually every other ship. But somehow it's more obvious when you hear BURNING LOVE.)
Kongou: The voices that echo across this boundless sea. Those girls' screams of horror, of lamentation, of resentment, and of their fear of death.
—"The Eventualities of Weapons That Learned to Love", by Ikezaki Misa. (Found on Danbooru, link not provided since Danbooru isn't safe for work.)
As they are pretty much people, what do you think happens to these girls when you 'scrap' them? Can you imagine 'crafting' one of them? There is a lot of implied Body Horror going on, such that some fanworks, especially the nsfw ones, go into great detail about the darker element of fielding what are basically heavily armed girls. Indeed, it's popular in some doujinshi to depict the girls getting arms or legs torn/blown off when their ship-selves take serious damage.
A very popular fan theory (so much that it's started to creep into a few official publications) is that the members of Abyssal Fleet are sunken Fleet Girls that Came Back Wrong as a result of their resentment for the carelessness or incompetence that caused their demise. And since Fleet Girls can be replaced by making new ones, it would be mean that, unless the Fleet Girls manage to wipe out the Abyssal Fleet with no losses, both sides would be condemned to an endless cycle of battles.
A lot of long time players know that it's nigh impossible to NOT get Fubuki before getting Nagato, Mutsu, the 4 Kongou Sisters and Kaga, and yet the anime shows that this is the first time the other girls seen Fubuki in the base. Doubled with the fact that she received her Kai Ni upgrade in January 2015, which only then gives reason for some admirals to keep her, fan theorizes that the Fubuki we saw in the anime may not be the first one to be posted to the naval base, but the first one to be used actively. Suddenly having Gen Urobuchi as a guest writer may not be too far stretched anymore.