Star Fox Assault's Aparoids were an interesting addition to the franchise, since they were something new and unique. Even though the problem in Adventures was pretty large scale, the Aparoids weren't focused on destruction. Instead, it was spreading across the galaxy if not the universe. The Aparoid Queen's goal seemed to be spread as far as possible, and create something new.
Based on the details about the Aparoids, I think that their presence was influenced by a genre of horror known as "cosmic horror". Cosmic horror is usually defined as the fear of the unknown, and involves a greater and existential problem that simple beings like humans or Cornerians will never truly comprehend what's going on. Trying to solve the problem however, will drive the characters insane since they're dealing with something no mortal should try to deal with . For an example, it can involve a godlike alien being that is far more intelligent than us and/or defy certain parts of our known reality. The Aparoid Queen doesn't seem to defy reality in anyway, but she definitely possess supernatural intelligence as well as superior knowledge. But as shown at the end of the game, Fox and his team come out sane.
What gets me more interested in the Aparoids, is the fact there could be something similar to them but different in many ways. For an example, it could be a being that is both omniscient and omnipresent, an object that warps reality around it, or merciless godlike beings that have motives beyond what a mortal can comprehend. Anyways, I like thinking about all of the possibilities on how Nintendo could expand on the fact something like the Aparoids could exist somewhere around the cosmos of the Star Fox franchise.
I would like to see your ideas on what Star Fox's next existential threat would be like. Is it an object, being, or something beyond our confined reality. Please keep you ideas original.