Yoshi's Island uses the SuperFX 2 chip which is very difficult to emulate. Even the first SuperFX chip has yet to have a game released for it. Add in that plus the fact that Nintendo has a huge library of good games to still give us (Super Mario RPG, Majora's Mask, Earthbound) and the usual problems with NoA and NoE, and you have Nintendo not wanting to devote the time getting the 2 games that use either SuperFX chip*
*Yes, there are more than 2 games that use the SuperFX chips, but Star Fox and Yoshi's Island are the only major titles that used them, the rest are either tech-demo style games or games that licensing would be a major pain (such as Doom)