When I think of secondaries, I don't just think of other characters that you find fun or enjoy using almost as much as your main, but characters that have positive match-ups against a number of characters that your main has trouble with. I want to get involved competitively soon, and while I find Pacman to be leagues of fun (almost as fun as Link), I wouldn't consider him my secondary because I'm not really sure how well he does against Link's counters.
For the most part, I think Elessar is right to say (as he did in another thread) that the metagame isn't really developed enough for us to be able to speak with clarity on his match-ups, and therefore a true reliable secondary for Link probably isn't deducible yet.
However, I think that for everyone but especially for those who main characters not considered to be in the upper crust of the cast in terms of viability, learning to play all the best or most commonly used characters is a good step - which for now looks like Rosalina, Sheik, Diddy Kong, Greninja, Little Mac, Ness, Lucario, maybe Zero Suit Samus. Even if we don't really find these characters fun to play, many of them are looking to have a large number of positive match-ups, and Link doesn't do positively against many of them, so maybe the best place to look for counters against individual characters within that layer is in that layer itself.
Those are my thoughts.