Because despite what you may realize, Pokemon Company, Gamefreak, and Nintendo aren't actually the same thing. Gamefreak is an independant third party developer (Who also develop non-pokemon games for other systems/PC) who happens to co-own the rights to pokemon with Nintendo (Who publishes the finished product and owns the trademark) and Creatures Inc. (Who manufactures the toys and TCG).
The three companies shares in the franchise are handled by The Pokemon Company, which handles most, if not all, of the licencing and advertising for the franchise to other companies. However, since pokemon is owned by three companies, and is managed by a fourth, this can become a little complicated when you want to licence something out. Whenever you do, you're not just paying Nintendo. You're also paying Gamefreak and Creatures, and they're going to want an equal cut of the profits, PLUS a little has to go back into TPC so they can continue to run the franchise.
Nintendo doesn't want to mix pokemon with their first party games because if they do, they would have to split the profit three ways, instead of raking in the profit themselves. Animal Crossing, as a first party game, makes money for Nintendo and Nintendo only. Pokemon Crossing, as a jointly-produced game, makes money for three companies, and is therefore not profitable.
