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A lot of people have issues with the Wanda character, how she's not allowed to go into The Dreaming by the Moon because she's biologically a man, how she dies, how when she dies she appears as an actual woman.
It's a load of nitpicky bullshit really. As Arion says, Wanda is one of the earliest transgender characters, it's ridiculous to complain about her. It's a great step forward to even have her appear at all.
Here's an article from someone who thinks the story was transphobic, some good points, but some nutty ones too: http://www.keepyourbridgesburning.com/2012/06/the-sandman-a-game-of-you/
The rules of The Dreaming must have offended a lot of people at one point or another, that doesn't make it an example of intolerance or anything like that.
To have Wanda there was a big deal, something most authors wouldn't dare to include in their stories.