I wanted to talk a little bit about the dynamics of this transformation type. Both probably merit a full "in depth" analysis and more, and both will probably get that in the future. But for now I wanted to give my brief thoughts.
I feel like gender change is popular because of the restrictive gender roles and gender expectations in our society. Specifically, I feel that male to female transformations are popular because of the restrictions we place on men's gender roles.
While the feminist revolution helped broaden women's gender roles - which is a good thing - we have not seen any movement comparable for men. Women can wear men's clothing without raising an eyebrow, but not the other way around. Boys are still teased for crying or acting feminine. I see a bit of hope with the new anti-bullying movement but I still feel like we are a long way off. Many men who don't feel manly can feel very out of place, especially socially and romantically. (I also feel like in subtle ways, our culture says that men are gross and women are pretty and sexy, but that's a topic for another time).
There are a few ways to resolve these conflicts of an unmanly man in the fiction setting. The standard way, which is employed over and over again in coming of age stories like Harry Potter, is for the man to 'become a man,' usually by turning into a warrior or an achiever of some kind. This in turn makes others respect him and women want him.
Another way these conflicts can be resolved in fiction is if the man becomes gay, which frees him from the constraints and expectations of heterosexuality. Or he could turn into a woman, which frees him from the constraints of being a man altogether.
None of these options are bad per se but I feel like there ought to be more available to the non-manly man, both in literature and in real life. There is a fourth option - for the man to accept himself as is, and be in a relationship with a woman who is also atypical in terms of gender roles. In both our broader culture and in the online story community this option is depicted only rarely. (If you know of one you like in particular, please lave a comment sharing it)
You may have noticed many of my stories contain elements of what might be described as role reversal among the couples. This is partly because I happen to really enjoy that dynamic and also to do my part to show that this is a viable option for men who feel like they do not fit into the 'normal' mode for relationships.
I do not yet have a single story that I can point to that describes exactly what I'm talking about in terms of this flip. I may never, in part because gender roles are so complicated that there is no one pure way to flip them completely. My story Relationship Realignment flips some aspects, while Graduation Day flips others.