Personally, I don't accept yaoi/yuri/genderswitch anime as evidence of diversity and tolerance in the medium, because it objectifies the people and situations in them. I'm a fan of yaoi, but I also understand that it is 100% objectification, and completely unrealistic. Yuri is sometimes nice to read too, but hinges on the idea of the "shoujo"- a passive and sexually immature girl- so yuri too is usually unrealistic.
Yaoi and yuri are popular, that's why there are so many. Not because anyone is tolerant or sensitive to gay and lesbian issues.
I don't consider Ranma 1/2 to be an anime about a transexual. It has a character that changes sex, but its not like he is a transexual like we might identify with. Ranma changes sex against his will, and his changes are played up for humor, titillation, and chauvinism.
PS, I love Ranma 1/2. I just think it's incorrect to assume our favorite anime are progressive. We don't love them because they are progressive, but because they are consumable and fun.
One of the reasons anime is so popular is because of the anime/manga consumer culture in Japan. Series are created in order to keep people watching, reading, and buying merchandise for as long as possible, and usually at the expense of a decent plot resolution or original forms of character development. But those "hooking" elements - moe characters, pervert humor, chronic miscommunication, high school drama, UST- are what make them fun, and make them a niche that anime fans, like me, enjoy indulging in.
Few anime are actually progressive. I think the anime I'd consider to handle gender issues in a thoughtful or realistic manner I can count on one hand. I think there are more RL movies trans people can identify with then there are anime they can identify with. I identified trans with characters in two anime EVER, Sailor Moon and Wandering Son.
That all said, I don't mean to negate what I said earlier about anime being accessible to gender variant people. Because anime is marketed at children and adults (though they are separate, often aimed at EITHER girls or boys, or women or men) they can deal with more complicated topics. You're more likely to see a gay character in a cartoon in Japan then you are in American because some anime are marketed to adults. And some, it turns out, aren't even played as the punchline.
Anime is not progressive as a medium, but within the medium, as in any other, there are gems that really reach out and touch us in the way art is supposed to.
Edit: Wow, do I sound bitchy or what? I find anime fascinating, but I also want to keep it in perspective.