Re: Never being accepted into Japanese society--
Japanese culture is by far less homogeneous than everyone makes it out to be. It is all a matter of comparisons. I currently live in Korea, which is actually more homogeneous than Japan. It is actually more difficult for weigukin to be accepted into society here than for gaijin in Japan. And believe it or not, you have more legal rights in Japan, whereas you have almost none over here in Korea.
It's all a matter of perspective. Compared to the US or Canada, yeah, Japan is a highly exclusivist society. But compared to where I am now, they are progressive and mildly accepting.
And guess what? Despite all these negatives, Korea isn't really that bad. In fact, I've been having a pretty good time of it here. The key is to judge people as individuals. For each person who looks at you funny and sees a dirty foreigner, there's another who wants to get to know you and five others who don't care either way. If I am having a decent time of it here, consider your experiences in Japan by way of comparison.
Secondly, regarding the whole anime line--
These shows are pretty much made by guys who started out on the fringes of Japanese society. Most artists and mangaka were otaku before they made it big. Hence, they filter society through a lens of how they want it to be. It can be considered somewhat subversive if you look at it a certain way. No, absolutely not, Japan is not what it is on TV, anymore than the US is, or Britain is. Goodness, if Korea was how it is on Korean TV, people would be committing suicide here on a regular basis, because life would be that depressing (it seems every TV show here is a tragic drama). TV reflects aspects of people's lives, social values, and cultural trends, but you cannot assume that TV is a direct portal to what life is like. It's highly distorted based on taste.
To tie both points together, I'd say that Japanese cartoons reflect what Japanese animators and writers dream about. It is fantasy. Indeed, this showcases their values, desires, and hopes. But one needs to realize that these things are only reflections of what is in someone else's head, not necessarily what is factual.
Besides, I'm proud of my homeland and I don't mind being seen as a foreigner. I AM. Being accepted by a small group of friends anywhere is enough for me. Why should I expect an entire society to drop and welcome me as one of their own when that doesn't even happen in my homeland? No welcome mats will be rolled out. Heck, if I travel to a different city or a different part of my own country, I feel like an outsider much of the time, and I still speak the language. It's all perspective, man. How you view yourself in your surroundings, and how you interact with them, is just as important as your surroundings interact with you.