StarFox is one of the many unloved children of the Nintendo family: while Mario gets a new game every other day, since Miyamoto declared he was done with the franchise after StarFox 64, StarFox has been pawned off to second and third party developers to dissappointing results.
The use of the Super FX, which made the 3D possible, is probably the reason the original game hasn't found its way onto the Virtual Console yet. Other notable games using the chip include Yoshi's Island, Stunt Race FX, and the finished but unreleased sequel StarFox 2.
Yoshi's Island, however, seems to be in line for a 3DS "threemake".