Androids or aliens who don't want to live with humans and fit in would probably not appear in Ultra series, that is not really the message that the series is trying to send.

That is kind of like the idea of rivals that often comes up in sports anime - a good rival makes you stronger. So a god villain will also make the hero stronger.
And I agree about the whole feeling sorry for the villain thing, sometimes the writers overdo it and it just doesn't work.