The settings can be combined by having Naruto characters appear in Eorzea. For example, the Hidden Leaf Village could be magically transported to a corner of Eorzea. The lush forests of the village could contrast with the more varied terrains of Eorzea like the deserts and mountains. Another way is to have areas in Naruto, such as the Valley of the End, take on some of the magical properties of Final Fantasy 14. Maybe there are floating crystals or strange magical auras in the Valley of the End now.
The settings can be combined by having the hidden villages from Naruto be located in different parts of Spira. For example, Konoha could be in the middle of a forested area similar to Macalania Woods. The temples in Final Fantasy X - 2 could also serve as important locations in the Naruto - Final Fantasy X - 2 combined world. They could be places where chakra or magic is especially strong.
One way to combine the settings is to have a portal open between Westeros and Middle - earth. Maybe a powerful wizard in 'Lotr' accidentally creates a gateway while experimenting with magic. Through this portal, characters from both worlds can pass and interact. For example, Aragorn could enter Westeros and help in the fight against the White Walkers, or Tyrion Lannister could end up in Minas Tirith and use his wits to deal with the politics there.
Maps can be used as a visual aid to enhance stories in educational settings. For example, when teaching history, a map can show the locations of important events mentioned in a story. This helps students better understand the geographical context and makes the story more vivid and memorable.
The settings could be combined by having a joint magical school project. The teachers from both Hogwarts and Halloweentown decide to have their students work together on a project that requires them to use the unique features of both settings. So, Hogwarts students might have to go to Halloweentown to study the growth of magical pumpkins, while Halloweentown students come to Hogwarts to learn about the history of magic in the wizarding world. This would give the opportunity for the detailed descriptions of both settings to be intertwined in the fanfic.
For example, the biotics in Mass Effect could be combined with the summons in Final Fantasy. A biotic user could enhance the power of a summoned creature like Ifrit. Or the tech abilities in Mass Effect could be used to upgrade the weapons in Final Fantasy. Garrus could help improve Cloud's Buster Sword with some advanced Mass Effect tech.
The cultural elements of the settings can also be combined. 'In the Heights' has a strong Latino culture, while 'Hamilton' is steeped in American colonial and revolutionary culture. There could be a celebration in the crossover where both cultures are showcased. Characters could learn about each other's traditions, like the characters from 'Hamilton' learning the significance of the Dominican Independence Day parade in 'In the Heights', and the 'In the Heights' characters learning about the Fourth of July celebrations in 'Hamilton'.
Another way is to have Naruto fuse his chakra with someone who has the ability to use Susanoo, like Sasuke. They could create a combined form that has the best of both their powers. The story could detail their journey of learning to work together and master this new form.
Well, you could have Hogwarts located near Forks. So, the students at Hogwarts might sometimes interact with the vampires and werewolves from Twilight. For instance, there could be a forbidden forest area that connects the two worlds in a way, and strange things start to happen when characters cross over.
The storylines can be blended by introducing the concept of chocobos in the Naruto world. Imagine Naruto riding a chocobo instead of using his normal means of transportation. Also, the idea of the Cie'th from Final Fantasy 13 could be incorporated into the Naruto world. Maybe some ninja are cursed and turn into Cie'th - like beings. As for the plot, it could start with a rift between the two worlds that causes chaos and forces the characters to work together to close it.
They can be combined through a portal concept. A portal opens between the Naruto universe and the Transformers universe, bringing Naruto and Arcee together. Then they can work towards a common goal like saving both universes from a threat that spans across dimensions.