I've discussed a potential re-release with Ash_Pokemaster. At first I was pretty adamant that the Mobile Adapter features might be restored since there is a Virtual Console game with Wi-Fi features (the original game didn't have any online features), but then I realized that the Wi-Fi servers for the Battle Tower and PCC would probably be too much hassle for Nintendo to handle just for a port. Unfortunately, we're past Crystal's anniversary, so it is more likely that Emerald will be given such special treatment instead (and I hope it will, to render remakes redundant).
I still don't believe Game Freak wanted to retcon out the GS Ball, because I don't see any reason why they would. As I see it, they knew that Celebi would be distributed at the tail end of Generation IV, so they only accommodated a movie-related event where the GS Ball wasn't needed since Celebi was directly distributed. In retrospect, they should have distributed the GS Ball in 2009 upon HGSS' release or Gold and Silver's anniversary, since they certainly had no problem to make Victini available before its movie. But still, I don't think they really wanted to get rid of the GS Ball.
What I'm hoping to see is a new game with the GS Ball event with actual time travel. After all, there probably won't ever be another Celebi movie, but it should certainly be re-distributed eventually.