Thinking about it, the biggest plot problems with the anime from my perspective aside from the obvious pacing and ordering issue of the episodes are mainly the handling of Fubuki's development in the second half, Yūdachi's Kai Ni and the lead-up (or lack thereof) and aftermath of Kisaragi's sinking. Overall I think the general idea behind it all can work, but it was handled poorly by the direction and storyboard. So with that in mind here's something that in my eyes would've worked better:
1) Increase Kisaragi's role a bit in episode 2. A possibility would be that she was formerly a member of the torpedo squadron who got reassigned to free up the roster spot for Fubuki.
2) Instead of Yūdachi's Kai Ni popping up out of the blue, perhaps tie it in with a bit of development for Yūdachi herself in the aftermath of Kisaragi's sinking. Here I'm thinking about something like the formerly easy-going Yūdachi starting to take her lessons and training serious to get stronger after Kisaragi (in the setting that she was formerly a member of the same torpedo squadron) got sunk.
3) Handling Fubuki's development more linearly en bloc instead of having her first gain flagship status and a tremendous success saving Zuikaku and Shōkaku before getting all depressed about the Kai Ni issue and the recall to base.
To reflect this in the episode ordering and pacing something like this would've been possible: