Unlike the Nintendo DS and 3DS, I noticed that the now defunct Nintendo EAD hardly, if ever, supported the Game Boy, Game Boy Color, or even the Game Boy Advance. There are some notable exceptions like Donkey Kong '94 or Link's Awakening, but for the most part, EAD mostly stuck to home console games.
Meanwhile, first party support for the Game Boy systems was largely carried by co-productions with Game Freak/HAL/etc., or other internal teams at Nintendo like R&D1 and Intelligent Systems. Hell, EAD didn't even develop a Mario game for the Game Boy systems, the Super Mario Land series came from R&D1, while the Super Mario Advance ports were handled by R&D2 I believe.
EAD wouldn't increase it's support for handhelds until the Nintendo DS, which was when they were restructured into multiple teams during that time. I think EAD mostly avoided the Game Boy line because the Game Boy itself was R&D1's baby, and they felt the need to support it more than Miyamoto and his team. Even going into the Game Boy Advance, it was largely R&D1 who carried the console first party wise.