I can understand the knee-jerk negative reaction. Granted a thorough examination of the feeling should reveal that it's not all that well-founded, but then again who waits to have their feelings until after they've analyzed them?
We're used to having a third game. Folks will buy one of the first two, knowing that they're missing out on a few aspects, but resting assured that the third game will come along in time and tie everything together into a single, satisfying package. When you split a game into two distinct versions, fans must choose between sacrificing a portion of the experience, or spending twice as much money for not nearly twice as much novelty. For plenty of kids, spending extra cash on Pokemon is probably not an easy option, and so buying only one of the two necessarily creates a feeling of having missed out on something.
Usually, the unification of the games in the third version ameliorates that feeling. Now that our "third version" is itself apparently split into two distinct games, the long-awaited reassurance of the game being tied together isn't there. Realizing that you're denied that attractive completed package is a let-down. It's not a wholly ridiculous response, although it is a 'glass half empty' sort of response.