Female Corrin is more popular because the overall concepts of Corrin's character seem more appealing to most people in the context of her being female.
Being barefoot is going to be more appealing on a female character to most people. For both aesthetic reasons, and more fetishy reasons (let's not dance around the fact that a large portion of the core Fire Emblem/Smash fanbase is now anime nerds/straight up otaku who love their waifus and have their fetishes, barefoot fetishes being very common in general).
Female Corrin also makes for another strong and powerful female character which lots of people want more of in gaming.
Also, there is an in-game reason as well - in Fates, it's impossible to get all of the child units if you play as Male Corrin. This is due to the fact that certain characters (known as "Corrinsexuals" in the fandom) like Shura and Jakob can only marry Corrin, and can only do so if Corrin is a female because they aren't gay/bisexual like Niles. Also, if you play as Female Corrin, you get Jakob in the beginning of the game and get Felicia much later, and vice versa. A lot of people consider Jakob a better unit because he can be reclassed early on into a strong physical promoted class like Paladin (since his stats favour physical stats and not magic ones, he's not very good as a Butler, which is his default class), and only requires a Heart Seal to do it, while Felicia is more magic oriented which means she's only useful as a healer. While she can be very potent later on as an attacker due to her high magic stat (she also has very good speed), it generally takes more work to make her an exceptional unit (I should know, I married her in my current Conquest run
![Stick Out Tongue :p :p](/styles/default/xenforo/smilies/tongue.gif)
). As a result, completionists, speedrunners, and high level players in general always choose Female Corrin regardless of their actual sex and gender identity.