In Japan, 3DS has already sold better than the PS3 (10 mill VS 9 mill) and it's already 1/3 of the DS sales (32 mill), adding an average 200k per week (
source, using info from Media Create), so, if anything, this game will boost the console a bit further. In Europe and the US, where the sales are a bit slower, it will be the step they needed to kill off DS and force people to move on.
There have always been people who couldn't afford buying a GBA and that didn't kill Pokémon after Gen II.