Suppose you're reading a story or watching an anime. The latter, at least, should not be a new occurrence for you. ^_^ The tale revolves around a princess, but we see her through others' eyes: her father, her pet lion, the boy who has come to love her... Who, then, is the main character? The princess, or those who are caught up in her story?
A few weeks ago, Gregory Marques argued that Jean Loc de Lartigue is really the main character of Nadia of the Mysterious Seas. Is this true? Granted, I haven't seen the rest of the series, but one shouldn't need to see a whole series to figure out where the action is. (Think: Rurouni Kenshin past the first few episodes. Title aside, it becomes obvious pretty quickly that Kenshin is the one to watch.)
In writing, sometimes a distinction is drawn between the main character(s), the point of view character(s), and the protagonist(s). While anime and literature are two different media, for the purposes of this article, I shall consider them both to be ways of telling a story, which is the important part. In Nadia, the main character is Nadia; there are many POV characters, but the most prominent one is Jean; and Nadia, Jean, and their buddies can be considered the protagonists.
Wait a second, you might say. Gregory's right: most of the time we're seeing Jean's take on events. How can Nadia be the main character?
Well, let's look at it this way. The main character is who the story is about. This is clearly Nadia, even if the story starts from Jean's POV. After all, who brings Jean into these adventures? Nadia. What keeps him in the story? Nadia. All the "bad guys" -- Grandis's gang at first, then Gargoyle -- are really after Nadia's heritage, Blue Water. In this context, Jean is important for his connection to Nadia, not for his ingenious inventions or the knowledge he's gained.
What about the point of view characters? They vary from Jean to Gargoyle to Nemo to Marie to... Completion of this list will be left as an exercise for the reader. Often, as has been noted, the POV is not Nadia. This doesn't necessarily signify that Nadia isn't the main character. One example of a similar technique is Arthur Conan Doyle's Sherlock Holmes stories. We see each mystery unfold through Watson's eyes -- but Holmes is the main character, the one who does the problem-solving.
The protagonist is the character we're rooting for -- and might not, in rare cases (though Nadia isn't one of them) even be the "good guy," assuming one exists. Since telling a story so that the audience cheers on evil people is difficult, you don't see it happen much. On the other hand, you might have an evil main character opposed by a good protagonist. For example, you could argue that Darth Vader (née Anakin Skywalker) is the main character of the Star Wars trilogy: he calls the shots and it is his redemption that leads to the Emperor's defeat. (If you add the upcoming prequel trilogy, you have the tale of his fall and redemption.)
So hopefully, we've established that main character, POV (the most fluid, especially in anime), and protagonist can actually be distinct. One question remains: why would any storyteller choose to make the three distinct, especially in this case?
One reason might be due to placement -- who's doing what, and where. POV characters tend to be strategically located so that they give you the maximum insight into what's happening in their world; if not, they're strategically located so that they give you clues but don't give away the plot twist at the end of the story. This would be the case in Sherlock Holmes stories. If we were inside Holmes' head, a fair storyteller would give us access to his thoughts, and that would ruin the fun.
Another reason is the reader/viewer's sympathy. It's a lot easier to keep your audience's attention if the audience actually cares about the character who's telling the story. This probably isn't an issue in Nadia, but in a story where the Evil Overlord is the main character, it might be important.
There's also tone -- Nadia is a moodier character than Jean, and her version of the story would be correspondingly gloomier. Or try to imagine what tone you'd get by showing everything through Gargoyle's POV. You might have a good story, but it'd be a darker story, and most importantly, it wouldn't be the same story.
All of this is speculation, of course. Only the producers know the real reasons. But in the meantime, I would hazard that they did have valid reasons indeed to name the series after Nadia -- and not Jean!