It has been quite a while since I've enjoyed a show quite this much.
Story: Socially awkward Yuki moves to Enoshima, where the hyper alien Haru appears in his life and keeps bothering him to learn how to fish. But then we discover that there is another alien being in the ocean whose power threatens to overtake Enoshima and possibly all of Japan during a typhoon. It was a fairly solid coming-of-age story; the whole point was Yuki's growth, and the whole fishing up JFX thing was the vehicle through which Yuki developed as a human being. Haru, if you know how to take a hint, is clearly on a mission from the very beginning of the story, so nothing happens that isn't set up. There were some loose ends and unexplained bits at the end, but otherwise I thought the story accomplished both its goals: Yuki grew, and the tension about whether or not the mission to fish up JFX would succeed was well-kept up.
Animation: I liked the color palate, as well as the art style. It wasn't as good as a Ghibli film or something that has more complexity of depth and perspective, but I liked it anyway.
Sound: That freaking song. "Haino haino haino, yoisho yoishona..." Fantastic. Duck noises = fantastic. Yamaaaaada. Enoshima/E-no-shima joke at the end. Fun stuff.
Characters: It would have been easy to make these characters flat and uninteresting, but they weren't. They each had strengths and weaknesses, and were very human. Yes, Haru is a bit annoying. Yes, Akira/Duck was a tad stereotyped. But the real triumphs here were Yuki, Natsuki and his family situation, and the blonde Duck dude who was convinced Akira was a traitor but then ended up believing in him anyway.
Overall: I think that this show did a great job of taking a fairly ridiculous story premise (alien in the sea causing the Bermuda triangle syndrome, threatening the whole of Japan) and making it into a quaint and human story of friendship and triumph against all odds. In fact, it's one of the better alien animes I've seen. And I also really like that it has that niche aspect that goes into more detail about the hows of fishing, without interfering with the storyline.