Ooh, I've seen previews for that movie (I think it's a movie and not an anime, anyway xD). It looks awesome, I'd love to see it.
But! Back on topic. Along the lines of Neo's "infusing with elements" idea, and with the "worship Pokemon as spirits" kind of idea, what if we did something like a bond between our samurai and one specific Pokemon? And their Pokemon powers up their weapon somehow. For example, a samurai and a Pikachu would make a samurai with a lightning sword. It'd be a little more difficult for people whose Pokemon partner isn't really an elemental type, but maybe we could have other effects, like a samurai with a Scyther might be able to move their sword faster/have a sharper sword, and a samurai with a fighting type like Machamp would have more force behind their sword, like being able to puncture metal or something.
With that, maybe we could tie in some kind of high tech sword? Like, to use it, the Pokemon is sucked into it kinda like they would be into a Pokeball, but from there their power can be used in the sword. And it would be limited to the Pokemon's own stamina--meaning you couldn't use the power non-stop. They might have to take breaks for a while, and during that time use it as a regular sword. Keeps them from being too uber. Of course, if you like uber, we can ignore that completely.
And lol, I thought everyone was talking about Avatar: The Last Airbender at first. THEN I figured it out.