Ok, several things that could make your character Mary/Gary-Sue-ish.
One, he should be forced into it somehow, like Deathsceptor said. And Darkrai... I'm not sure if I like the entire "legendaries-getting-murdered-by-one-another" thing. Maybe Darkrai was corrupted by someone or something that awakened him, and then
he took over the ordinarily peaceful Mew.
Also, I was pretty sure that Ho-Oh was the mirage Pokemon, not Mew. Maybe it's just me.
Why does Darkrai want the main character to suffer? Maybe Darkrai has something to do with his father... Darkrai's main target shouldn't be solely the hero. And this Ninetales... maybe she could be a vessel of evil that Darkrai uses, but then changes her mind.
I'm really bad at giving advice...
I'm trying to give you some ideas, though, to help flesh out the plot. Of course, it is your story; it's up to you to breathe life into the characters and tell their stories in a way that's believable.