Do I got a story for you! GameFreak actually does care about Adventures a lot! In fact it's probably GameFreak's second or most beloved adaptation. In fact, in some ways they are responsible for Pokemon Adventures long-running freedom of creativity, something the anime somewhat lacks from time to time when having to market the games. It's not only Pokemon's second biggest longrunners, behind the anime, and earned unique praise from GameFreak that not even the anime gets. but like the anime where GameFreak creates concept art in how a Pokemon moves and behaves, GameFreak and the writer of Pokemon Adventures cooperate quite a lot, I believe three months, not really sure I just know it's pretty early, before the games actually release, to get the story that GameFreak envisions for the games right with the creative freedom of course, sometimes far better than what GameFreak puts in the games like the Ruby and Sapphire arc. It's why the huge amount of game detail Kusaka puts in Pokemon Adventures is so insane. In fact, I actually don't know a lot of other Pokemon mediums that get the kind of same strong support as the anime and manga.
In fact many fans believe GameFreak and it's partners have taken inspiration from Pokemon Adventures. Pokemon fans have noticed that Ash and Serena's relationship seems a little too similar to Red and Yellow's relationship, have noticed that AZ's background is a lot similar to the Mask of Ice. However arguably the biggest similarity that even doubters have to admit is quite interesting would have to be Black and White's story being quite similar to the Yellow Arc, like characters having the ability to talk about Pokemon, discussing the Yin and Yang of industry and nature, the villains wanting to liberate Pokemon, how N and Ghetsis reminds people of Lance and Agatha etc or how Yellow's relationship with Lance is similar to the player character's relationship to N. I think this has to do more with the fact that the majority of Pokemon fans, especially in the west, still identify Pokemon with the anime, which is the marketing tool for Pokemon's popularity. For example, lots of people still think the original main protagonist of the series is Ash, not Red. Now that I think about it, the anime is really the only other medium to have the luxury of being referenced in the games.
So in general, GameFreak does care about the manga but in terms of popularity, the anime is a more profitable marketing tool to identify with in the games. Still it doesn't mean they can't include a few "silent" cameos that only certain Pokemon fans may know, if you know what I mean eh?
