Definitely going with Male Miqo'te. I couldn't care less how popular it will become. I have wanted a Male Mithra since FFXI. Hell a LOT of people who picked Mithra would also have chosen a male version back then if the option was available. So you'll see a flood of Male Miqo'te because Miqo'te is already popular.

This worry is like saying "Damn, I'm not going to pick Human even though I love it the most, because it's popular".

Just pick the race you WANT to be. The hell with whoever else wants to pick it.