Of course, there is nothing really preventing Malladus from the game. He could have left Hyrule to conquered new Hyrule or was banished and sealed at New Hyrule. Saying he only exist in New Hyrule and thus cannot appear in a new game makes as much sense as saying Ganon died in ALTTP and it is the final game. What I mean is that Ganon died in ALTTP with no hint of resurection and then he appears the LOZ with no explanation at all. Some may shrug this off with a ressurection ritual that happen in between, but if that can happen to Ganon, why not Malladus? This is the universe where anything can happen, such as computers, phones and robots exist in a medieval game.
As to why would Nintendo bring an unimportant, why not? In the first Zelda, Ganon was a generic evil prince of darkness that invaded Hyrule. He had no personality aside from being evil and being prince of darkness suggested that he is just one of the many evils in Hyrule as opposed to be King of Evil. It wasn't until ALTTP and OoT that Ganon became the villain we know and love. It's better to develop an existing villain in future games than it is to make new villains with blank slate. Vaati started off generic evil kidnapping eyeball and look how he developed in the prequel Minish Cap.
As for Malladus, to me, he's been something that I cannot ignore when theorizing Skyward Sword. I've tried my best to avoid him and see other possible villains of Skyward Sword but ever since Ghirahim is called a Demon Lord, I can't help but wonder if there is a connection. When the intro came, it resembles ST's backstory to a degree. Both had an evil Demon leader that destroys everything with an army and fought a war between good and evil. Then I saw Ghirahim's Master and I wonder why his face looks familiar. I compared it to the Demon Train from Spirit Tracks and realized that the head of the Demon Train bears more resemblance to Ghirahim's Master than Ganondorf, who was believed to the ST because of that face.
Overall, I'm still not a 100% sure that Malladus is the main villain or would even appear at all. Normally, I would keep my ideas to myself in fear of being pronounced wrong. But after seeing other people suggesting it, I decided to give my own thoughts about this. I might be wrong and maybe the main villain is someone else but hey, it's fun to theorize new ideas.