It’s a brilliant icon, as I’ve thought since the first time I saw it. It’s not just a fish, it’s a fish looking and/or moving upward—just what “meta” means in the context of software: “a prefix added to the name of a subject and designating another subject that analyzes the original one but at a more abstract, higher level” (Dictionary.com). “Metadata,” for example, which is data about data.
The fish in Meta is going above (in the sense of subject matter, not superiority) the general and social Q&A levels to questions about the site itself. It’s much easier to show direction of movement with a fish than with a jellyfish.