I do not think it is likely, because Malladus was an enemy from Spirit Tracks, set very far in the future of the series on the Adult Timeline. This game is a prequel to Ocarina of Time, so the evil we face is likely to be older than Ganondorf, not newer. I believe that the final boss may be the leader of Ghirahim's tribe. They might be the "dark interlopers" spoken of in Twilight Princess, from whom the Twili are descended. He might be the one who tried to challenge the power of the Gods.
However, there is no saying that Malladus couldn't be in this game. It's possible that Malladus was sealed throughout all the previous games, and was only unsealed long after other evils had come and gone. I really wouldn't have imagined this myself, but I can't say it isn't possible. There just isn't enough evidence to say anything confidently either way.
If Malladus is in this game, though, it would be fascinating to see his origins and how he came to be sealed in the first place. There might even be backstory on Chancellor Cole and the Lokomo. It would also mark the first time a major character from the handheld series reappeared in a console game. Nintendo usually only moves in the other direction, putting console characters into handheld games.