Only having read volume 1 of the Invisibles so far, my concerns with Morrison's portrayal of the trans character Lord Fanny are minor. Mostly, "Lord Vagina" is just a tacky name...However, she's treated normally by everyone (except the douche-y homophobic and transphobic teenage new-recruit. I assume his character becomes less insecure-90s teenager as the series progresses.)
As far as trans women in fiction go, Wanda could be worse. Could be better too. Mostly, I think Neil Gaiman does a good job writing Wanda and where her dialogue is stereotypical, most of the time it can fairly be marked up to early 90s "innocent" ignorance. As far as the bigger picture goes, I think Gaiman shows where he falls on the issue in the panel where Barbie crosses out Wanda's birth/given name on her tombstone and writes her real name: Wanda.
The art is much more bleh, though. Once again, it was the early 90s...Maybe the artists would portray her differently if this had been written in the past few years. Still..bleh to the art.