... all the similarities between Ninja Scroll and Pokemon Master are intentional. Ace actually mentions in the author's notes for the first chapter that he wanted to make Pokemon into a story 'like Ninja Scroll', which apparently entails ripping off the plot point by point and then forgetting about it entirely in roughly chapter 6.
There's also tons of ripoffs from Rurouni Kenshin and Xenogears, too. And the latter is frightening, given that Xenogears is a very long and drawn-out (if enjoyable) EVA ripoff.