I don't know why, but once I get the blue tunic, I keep it on for the rest of the game, simply because I think it looks cool. Between the two system, I like the 3DS version of the tunic better.
I haven't played the 3DS version but I always liked the classic green tunic. Green is my favorite color so that probably played a role, but I think green fits Link the best.
To me, I like the Red and Blue because the Red goes great with Link's final gear. I like the Blue becuase it looks cool with the Hylian Shield and the Master Sword.