That, and there actually
are manga and anime where trans people are portrayed sympathetically and rather realistically, like
Wandering Son and
Bokura No Hentai (no, it's not hentai, the english translation of the name is "Our Transformations"). And honestly, from the look of things, I doubt that series like
Gen Zed and
Assigned Male handle transgender issues better than these series.
Edit:
I should warn you that numerous wikipedia editors consider "transgender" to be an umbrella term that also includes gender non-conforming people, so some of the series listed on that page might be about cross-dressers and etc. and not transgender people in the sense that we know.