In all honesty, all they did was re-design the playable girl trainer for the Johto games.
Her Crystal design was really awful (green hair in some space-anime hairdo wearing a kippah?) and not up to standards with the girls after.
This re-design is much better than what the girl looked like in Crystal. She even has the same kinda hair-style (but not as weird looking) with better clothing.
It's not like these trainers are actual characters, they're just an avatar to be used to play your adventure (hence why they even bothered to add in a girl trainer so females playing wouldn't be left out).
I don't really get how you can "replace" a "character" that never really existed in the first place.
I also never get why people call them such names like "Gold", "Kris", whatever. They don't have names, they're YOUR avatars in the Pokemon World.
And no, the Pokemon Special manga is not a canon thing of the Pokemon World. Just because a few TCG cards use "ideas" from it, doesn't mean anything.
IMO, the manga does a very poor job of conveying the Pokemon World.
In reality, every medium is a separate thing from each other.
Fun fact, it's official. If it weren't, it wouldn't be published here.
There is many other Pokemon manga that have been made and translated into English. Its very easy for someone to get the "OK" to make a manga/comic based on anyhting. To me, all the manga are "unoffical" and "fan-made". What makes one manga more official over another?