The difference being those games are new. Their only prior release was on a console few people had, and fewer actually played. Additionally, the games are still market valued at about that price, while Link's Awakening's most recent releases included 3 USD and free (depending on when you got your 3DS).
Would you say 60 USD would be a fair price for a NSMB U style graphical update of Super Mario Bros 3?
It was at a time considered the greatest game of all time, and remains more highly regarded than Link's Awakening.
How about Sonic the Hedgehog?
My point isn't whether or not $60 is worth it, my point is Nintendo is Nintendo and all "logic" goes out the window when it comes to their pricing. Nothing new, not sure why $60 is still a talking point. Pretty obvious MOST of their first party titles are going to be $60, port, remakes, and all. Pokemon Let's Go all but confirmed this for us...