Some popular tropes include the 'unexpected friendship' trope. Characters from Naruto and Fire Emblem who you wouldn't expect to get along become close friends in the harem fanfic. The 'training together' trope is also quite common. They train to improve their skills and in the process, their relationships deepen. And the 'mystery element' trope, where there's a mystery in the harem setting, like a hidden power or a secret about one of the characters that the others have to figure out.
Well, a typical trope is the 'rivalry - turns - to - love' one. In these fanfictions, two characters who initially compete for the protagonist's attention end up falling for each other. Also, the 'protector' trope is seen often. A character from either Naruto or Fire Emblem will take on the role of protecting the others in the harem, which helps to strengthen their bonds. There's also the 'culture clash' trope as the two different universes have their own unique cultures that create interesting situations when combined in the fanfic.
One popular trope is the 'fish out of water' situation. For example, a Naruto character might find themselves in the Fire Emblem world and have to adapt to its different combat styles and social hierarchies. Another is the power - up trope, where characters gain new abilities or powers through their interactions in the harem setting. And of course, the relationship - building trope is common, with characters slowly developing feelings for each other over time through shared adventures and challenges.