SO apples and oranges, chihuahas and whales, and fans being fans aside, it all matters on perspective.
In terms of creativity, Pokemon is a winner because of it taking the standard RPG idea and twisting it into a completely new subsection, which inspired many more game designers to have their players "catch 'em all".
Call of Duty is also good due to it being an insanely succesful series that is able to appeal to almost anyone. Yes, I am aware of previous shooters such as Doom and the wildly popular Halo series, but Call of Duty practically made people aware of itself since, well, the CoD games are enjoyable.
However, there can't be a definite winner in this debate. Each game is a winner in categories that correspond to them, but the two cannot be correctly matched against one another. Claiming one has better graphics is just plain idiotic due to one series being mainly portable and the other on home consoles. Gameplay solely is based on whether or not you like to strategically plan out how to use your team and change it, or try to rack up as many kills as you can with whatever strategy you see best. It would be like comparing Mario to Halo, it makes no sense.
Well, those are my two cents. I'll leave you all to your quarrels and whatnot.