As for my thoughts on the series as a whole, it began as a promising story of a high school girl’s entry into a dangerous world that appeared to be wonderfully constructed. As the layers came off, it became much easier to see that there really wasn’t much beyond that. The danger never really appeared but twice (the first episode at the cafe and during the dinghy race), but each was rather easily resolved. At about halfway, the slogan for how the plot worked appeared in the form of “everything works out when you’re a pirate.” From that point on, the drama ended and plots that simply passed the time began. I’m also aware that the last 6 episodes were entirely anime-original material, but I think the story had lost its way far before then. In conclusion, by constantly avoiding anything that could disappoint its audience, Mouretsu Pirates became nothing more than a weekly running joke about easily resolved plots and wasted potential.
Ouch.
I know the answer: the anime is an adventure for little girls, and it is not supposed to be a game of guessing who survives to the ending credits. If you want that, watch Gurren-Lagann (spoiler: Yoko lived).
SDB even threw out his fridge for the sake of this anime, around ep.14:
And that's the secret to the appeal of Mouretsu Pirates for me. I'm no longer expecting a tight story, or deep plotting. [Emphasis mine — Author] I don't expect it all to make sense. This isn't like Shingu. But Marika is a fascinating character, and the Hakuoh Academy is a wonderful place, and the supporting characters are all amazing, and well just damn; I like visiting it and spending time with them all, even if the story isn't tight and the situations are somewhat contrived.
I only wish it worked for me too.
UPDATE: Jonathan Tappan remarked that Mouretsu cannot be a story for girls, as I posited above, because it does not follow shoujo tropes. I am not sure I agree. There was anime before that defied the 4-quad taxonomy of shonen/shojo/josei/seien.