I was watching Firefly and had an idea, what if the show is done with characters from MLP? So I went through the list of characters and judging by personality traits decided on which characters played who and this is the list I came up with.

Mal - Sunset
Jayne - Rainbow Dash
Wash - Pinkie Pie
Kaylee - Rarity
Zoe - Applejack
Inara - Fluttershy
Shepard Book - Discord
Simon - Twilight
River - Starlight

I chose these characters based on comparing the personality of the characters on the ship and the characters from the show. I also thought about renaming the ship Harmony. Are there any stories done with an MLP Firefly crossover? If not would anybody be interested in writing one with the character list like this.

Sounds good but, I think I would switch Rarity and Fluttershy.

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I chose those specific roles because Fluttershy is the kind gentle type but isn't afraid to stand up for her self like Inara, and Rarity is the dreamer like Kaylee. Plus I can't see Fluttershy as a detail oriented engineer where as Rarity has an eye for detail that would fit with Kaylee's style of engineering. The ability to see what's wrong with the engine after a glance.

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Given that, it makes total sense, and your selection works well
I might be a bit biased because I can’t stand Inara and FS is one of my favorites. (As is Kaylee)

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They're both my favorite characters in their own shows as well, Fluttershy taking a front seat to anyone in either show as my absolute favorite, and I can understand being biased. After all if I went with the more obvious pairings that would just create a difficulty trying to override natural personality with whatever character match them with on Firefly. I can't really put Twilight in the captain's chair because her trying to play Mal, when she doesn't have a commanding I know what I'm doing attitude, would be so far removed from anything she would do it's not even funny. Where is sunset in the very first movie had a commanding personality and isn't the kind of person who would hesitate and try to overthink the situation, she fits better as the captain of the ship. And that's just the first example I could come up with.