Pokexalted/Setting
Pokémon is sort of postmodern in terms of technology, and a lighthearted world where everyone plays by the important rules even while they're breaking the law. It's a far cry from the wild fantasy langue of Exalted. It includes: bicycles, ocean liners, an internet... hell, it probably has a space program kicking around somewhere.
Of course, you don't have to throw in all that crap. Pokémon are ultimately no stranger than many other things to cross the borders of Creation - they'd fit right along side yeddim and aubrochs as nasty native things with sharp pointy teeth. It's really your decision about just where you want to draw that line. But: given these two points, I've got a few ideas to throw out.
- Abrupt Introduction Theory
The most realistic approach (or the one least likely to futz with continuity) would be to in some way introduce the Pokémon themselves into the Realm on the fly. From the four poles issue a new kind of nature, a strange and vigorous multitude seeking a place in this new world. Already besieged by the anathema menace, how would the Realm handle this? Would they coerce the demons to fight by their side, take the place of frail human slaves? Would they seek to subdue this new force? Maybe the Lunars would decide they have a new ally...
With this approach, Pokeballs may not even exist - or they may be a new development akin to hearthstone amulets, designed by sorcerors to tame the natural strength of these new monsters. The concept of "trainers" would be a new revelation, and one shocking to most mortals raised on the idea that no fool would try and raise a monster - but for the underpowered or underpriviledged, a fast road to strength.
- Lost World Theory
http://www.teamrocket-video.com:26005/rebirth/map.htm
The next approach is to consider the Pokémon world as existing alongside that of Exalted. Not as in some parallel dimension crap, but literally alongside. What's beyond the Coral Archipelago? No one knows. But that's a whole lotta ocean - and the world of Pokémon is set on a series of islands. Maybe if you get far enough west, you'll bump into them. Travelling between these two canon settings allow any number of "first contact" scenarios, but runs the risk of hopelessly entangling what are ultimately two seperate genres. A grim and embittered Dawn caste meeting a bright and spunky 13-year-old Pokémon trainer is a punchline, not a dramatic scene!
If you feel like lightening up the Exalted scene, or taking a noir approach to Pokémon (and who hasn't?) this is still feasible. After all, it wouldn't take much to treat Exalted as an anime teen drama... Tenchi, anyone? And mix those mental images of Pokémon cities with your last run through Deus Ex or Max Payne. Quite acceptable either way.
- Inexplicable Integration Theory
This one starts really mucking with Exalted as stands. Just throw Pokémon in. Not as a role-played process, a gradual evolution of society and values, but... "Bam! There are now Pokémon everywhere. There just are, get used to it." Given a Pokémon's function as pet, beast of burden, and/or trained guard, this isn't all that farfetched and does save the GM the trouble of coming up with reasons for things to be the way they are. Enterprising GMs may also want to simply switch nouns around... the many professors who study Pokémon, for instance, can be replaced with sages and monks. Stuff like that.
It could be silly at times, though. Players of the games will expect to find certain elements present that will either unbalance the game or clash with the GM's vision of the world. This is always a problem with any setting that isn't purely homegrown, but all the same - working with a beloved IP like Pokémon will just exacerbate the problem. Anyway... airships for cruise liners, Exalts for gym trainers, you could throw something together.
- Stand Alone Complex Theory
Finally, there's always the option of throwing out Exalted altogether and just running a Pokémon game with the Storyteller system. No Solars, no Realm, just get on out there and do whatever you feel like with the other stuff. You could even keep a certain amount of Solar for panache and tactics - remember, Power-Awarding Prana is the master trainer's friend. Charms that only work when granted to a Pokémon would make for an interesting, CGI-laden bloodsport...
The ExMod would probably be a handy resource for this (or this, a nifty thing to plug into the ExMod), or for the Lost World Theory. You might also want to consider using the new WoD skill sets instead of Exalted, for a pure Pokemon game. Yes, that's right - this is also WoD compatible. I think. I'm not too thrilled with some aspects of the new WoD... anyway, you can tell by now I don't have any intent of spelling things out for you. I'm just throwing out seeds, and if any of them sprout? Good luck, tell me how it goes.