Well... in my own university experience, I've taken a couple of women and gender studies courses. Trans issues and the ideas of gender identity are not frequently mentioned to be honest. In general, they may make passing references in relation to the social construction of gender, and of men and women transcending gender boundaries, but trans-centric topics or courses are extremely rare.
There's a course I've wanted to take called the psychology of gender, it hasn't been offered in ages. There's one class out of 50 on my schools course list that makes a mention of trans anything.
Now admittedly, transpeople are a very very small minority, but I'd always thought it would be a very insightful area of study that would reveal a lot about sexuality and gender.
I don't know what people are saying about it, but I go to a large, fairly progressive university that is generally very up to date with all their course offerings and teaching material, and trans topics have hardly made much of a mark. There's a little bit of academic discourse I'm sure, but I think its severely hindered by the relative lack of actual transpeople in academia.