I dunno, I kind of see a difference. Call of Duty is primarily a multiplayer game, whereas Pokémon is a JRPG. In a new CoD, people are looking for a refinement of the multiplayer experience. People expect more "new" in a JRPG, especially in the story. Black and White in particular were praised for telling a great story within a Pokémon game, pretty much a first. If BW2 doesn't live up to its predecessor where plot is concerned, I'm not surprised it's receiving a lukewarm reception.
That said, White 2 is going to be my first Pokémon game since Crystal, so I don't care how similar it is to White. It'll (almost) all be new to me. But of course, you should focus on the reviews themselves rather than the scores. Generally, even if Pokémon gets a low score, it's for being too similar to a previous iteration, not for being a bad game.
