Power - up and evolution is also a common theme. In the Metroid series, Samus has different power - ups and her suit evolves. In Naruto, the characters grow in power through training and new jutsu. In crossovers, often Naruto will experience something like a power - up similar to Samus' suit upgrades, or Samus might learn about the concept of chakra and use it in a new way, which ties into this theme of power - up and evolution.
In such a fanfiction, the story could be set in a new, unexplored part of space that is somehow connected to both the Star Fox and Metroid universes. Samus could be on a mission to investigate this area when she runs into the Star Fox team. They initially have some misunderstandings due to their different ways of operating, but eventually, they realize they need to work together. The plot could include epic space battles, exploration of ancient ruins filled with secrets related to both franchises, and character development as they learn from each other's skills and experiences.
A cool concept in Metroid Prime crossover fanfiction is the combination of different power - up systems. For instance, if Samus were to cross over with a game like Ratchet & Clank, she might get access to some of their wacky and powerful weapons, while they could get a taste of her Morph Ball ability. It could also be interesting to see a crossover where Samus meets characters from the Mass Effect universe. They could exchange technology and knowledge, and Samus could learn about biotics while sharing her knowledge of Chozo technology.
Obviously, Fox McCloud from Star Fox would be a main character. He's the leader of the Star Fox team and a skilled pilot. And Samus Aran from Metroid is a must - have main character too. She's a badass bounty hunter with amazing combat and exploration skills.
One interesting concept could be the combination of Mega Man's robotic abilities and Samus' exploration skills. For example, Mega Man might use his arm cannon in the more maze - like environments typical of Metroid games. Another concept could be the meeting of their respective villains. Dr. Wily and the Space Pirates could form an alliance, creating a greater threat for the heroes to overcome.
Samus is the central character, but characters from other Nintendo franchises are popular too. Mario could be an unexpected but interesting addition. The contrast between his jolly and simple - looking appearance and Samus' high - tech badassery would be quite something. Additionally, characters like Solid Snake from Metal Gear Solid can be included. His stealth and combat skills could be combined with Samus' exploration and combat abilities in some really cool fanfiction scenarios.
One idea could be a Metroid crossover with the Legend of Zelda. Samus could find herself in Hyrule, facing off against Ganon's forces while also dealing with Metroids that have somehow made their way there. Another idea is a crossover with the Mega Man series. Samus and Mega Man could team up to take on a new threat created by Dr. Wily and the Space Pirates combined.
Definitely Mega Man and Samus are the most popular. They are the main protagonists of their respective series, so it's natural that they take center stage in the crossovers. Their contrasting yet complementary abilities make for great storylines.
There's a fanfiction where Naruto gets teleported into the Metroid world. In this story, he has to adapt to the new environment, learn about the Metroids and their powers, and use his ninja skills to survive. It's a really cool read as it shows how Naruto's chakra control could be used in the context of the Metroid world, like when dealing with the various alien creatures and the advanced technology there.
Master Chief is often a popular character. Given his significance in the Halo universe, it's natural for him to be a central figure in crossovers. He has the skills and determination to face the Flood threat. Another one could be the Arbiter. His unique perspective as a former Covenant and now an ally in the fight against common enemies makes him an interesting addition in fanfictions involving the Flood.