According to Joystiq.com the reason for the red cases is that six Mario games (New Super Mario Bros., Mario Kart DS, Super Mario 64 DS, Mario & Luigi: Bowser's Inside Story, Mario vs. Donkey Kong: Mini-Land Mayhem!, and Mario Party DS) will be re-released in red boxes, to "make it easy for [consumers] to find their favorite Mario titles."
No price drop was announced for the games, so its just looking like Nintendo wants Mario titles in red boxes.
I wonder how long till the Wii Mario titles are repackaged in red boxes too...