I don't recall reading about any developer interviews stating they want X and Y to be like the anime series.
I'm also not sure what cel shading has anything to do with making a Pokemon core series game like the anime. There are countless video games out there that use cel shading.
Fire Emblem uses cel shading. Anime? Sure there was a Fire Emblem anime in 1996. But the choice to use cel shading since 2005 has nothing to do with other forms of media.
Cel shading is simply an artistic technique to allow for 3D rendering. XY are the first 3D Pokemon handheld games. I don't see how that has anything to do with the developers supposedly wanting to make the two games like the anime. Because if they did, they sure as hell failed miserably.
Now answer me this, what games did the orange islands promote again?
In Japan, Pokemon merch is often released around the same time a particular series of episodes are broadcasted. Kids watch the anime, the anime end slate advertises upcoming products/events, the kids ask their parents to go buy.
Merchandise is not exclusive to core series games. Toys, trading cards, gadgets, events, you name it. They all count. I'm sure if we looked hard enough back to 1999-2000, we'll find an assortment of merchandise in Japan related to that Orange Islands season.