You'd need to decide how to handle pokemon race/classes, though. Unless you mean to have humans and elves running around in the same plot (do these games have a plot? I don't honestly know).
Yes it has a plot, and I had an idea for how to handle this. I was going to restrict the playable races to the humanoid pokemon only, and maybe the others depending on biology, and whether they can pick up a sword or not. In the pokemon games your pokemon could have four moves, so I thought it would be interesting if each playable race had four daily moves which can all be used once a day (EX: a charmander gets one fireball a day, a snivy level 1 wizard would of course get the standard 2 fireballs a day, but a charmander level 1 wizard would recieve a total of 3 fireballs. But one is his racial daily, so it runs off his charisma as opposed to his other two which run off his intelect)
I'm not really convinced it would make a decent campaign setting, and the work needed to craft a way to convert a bunch of 'mons to the GM's system of choice wouldn't be worth it. Perhaps the plot minus mons would, but not the setting. :/
I was just going to run them as normal monsters/npc's.
http://bulbapedia.bulbagarden.net/wiki/Arcanine_(Pokémon)
Pretty much, its a fire tiger, best way to describe it.
http://paizo.com/pathfinderRPG/prd/monsters/tiger.html#_tiger
And all I have to do is give him some fire resistance stats, and a daily fire ability, Fire Breath
http://paizo.com/pathfinderRPG/prd/advanced/spells/fireBreath.html#_fire-breath Seems to be a great fit.
As for the NPC's (Humanoid Pokemon/bipedal Pokemon EX: Gardevoir, charmander, snive, ect) after their dailies are used, their just whatever class they are, warrior, wizard, bard, ect. A little fine tuning would be preferable, perhaps the players and npc's start with one daily and gain the other three by achieving a certain level, but I can see it working after some fine tuning. An example could be this EX: player Robert is a level 1 fighter named Drake. He has one fireball which is based on his Charisma as his racial daily ability, but after it is used, he relies only on his fighter skills, his feats, his armor and his weapon/'s. He wields a greatsword, in character he says it was made from the remains of his childhood pet aron. He wears scale mail.
Hes on an adventure with his friend Bruce, whos playing Flos, a female Kirlia Wizard. She has one telekinesis ussage as her racial daily, and as a level one Wizard she has 2 fireballs. She is not proficient in any type of armor so she dawns a yellow robe. She carries around a quarterstaff but keeps a light crossbow for when her spells run out.
Though, I think this could use some fine tinkering (And tell me if I got some basic stuff wrong in there like level 1 wizard spells, its been a while since I used Pathfinder core rulebook.) But I think this would make a fun compaign, what do you guys think?