That sounds sort of cool, definatly original. Try and make an elaborate culture around the Merpeople first (including their relationship to the pokemon), maybe a conflict can arise out of that. For starters, they will probably speak a different language than the humans and a fight could break out there from mis-interpretation, especially if they have rituals, traditions, etc that seem hostile to the humans.
The war could also be over something pokemon related I guess, perhaps the merpeople would be against capturing pokemon in the ways that the humans do and cause an uprise to try and free them. Or maybe they don't have pokemon and want them from the humans.
Or it could just boil down to regular old human greed. Think of a Giovanni-type character that wants to harness the power for himself (*cough*mewtwo*cough*) and have his team go down and exploit it. It's sort of been done before but I guess it could work.
Like I said, it's definatly a unique idea it might take a bit of tweaking and a lot of thinking to make it as a role play though in my opinion. You can definatly do it but you'll just have to get creative with it and think a lot about the culture of the merpeople and also find a way to tell the players about all of it. Once you've got that down, thinking of a motive for the war shouldn't be all that hard. Good luck, I hope I helped and gave you lots to about