@browncoat - Most of the transformation fiction stories I've read have actually been somewhat feminist, because they usually deal with some kind of gender transformation. Either a man into a woman or vice versa (or sometimes both).
They are usually fairly lighthearted though and honestly, I think that might be because when you come right down to it, men and women aren't all that different under the surface. There is only so much depth you can give to someone being horrified that they have to wear a bra.
I do think there is space for more though. One of my favorite celebrity stories is the one where Dustin Hoffman describes his transformation in Tootsie and how they turned him into a woman and he realized that he wasn't attractive enough to invite his own interest, even though he was intelligent and funny and so forth. And it made him realize the different pressures women face in society. Which I think is the point of transformation fiction. To throw light on a different viewpoint.