The reason why this was implemented into animal crossing in the first place was because back when the gc was popular there were no other methods of playing or obtaining retro Nintendo games other than trying to find a (rare) copy of one. Now that we have the 3DS' virtual console and what not it just seemed unnecessary to add it.
The devs were concerned about these retro games and thought implementing them in the GC animal crossing was not only convenient and beneficial for its own unique consumers but also the pre-existing fans of retro games, thus bringing even more appeal to the first implementation of the growing franchise!
Personally, I didn't really like the retro games in the GC ver. As fun as some found them, I thought they drew attention away from the original content of the game. Less "let's play ac for its totally unique characteristics!" and unfortunately more " I can play retro games? COOL! Ill primarily focus my time on playing the retro games, screw the actual game's storyline!"