I always looked up to Ruby from Pokemon Special. There's no other person that can appreciate something beautiful as much as him. He's a feminine type of male, kinda like myself, and he's rebellious enough to run away from home to chase his dreams. I like him especially because he has a hidden strength for Pokemon battles too.
The first Pokemon Special volume I read was 17, which shows most of these characteristics of Ruby that really made me like him as a character. The scene where he fights his dad on the weather institute was especially awesome XD
I did get to love a lot of the other characters too XD
Gold is really awesome (obviously) and there's something about Pearl's nature that I really like.
For the female protagonists, I'm not so sure because I usually look for role models in favorite characters.
However, I can say that I like Blue because she's mischievous and powerful, Crystal, because she's so straight edged XD and Platina, because she's drawn so beautifully in the manga haha