It's not so much linking the two. People just simply don't want to accept the two eras as connected. People are constantly separating Pit for example. They don't want to accept that NES/GB Pit is the same Pit that was in Uprising.
Sadly most this is all based on their own personal head canon that either Uprising or original Kid Icarus clashed with, so they do the ignorant thing and say 'no I don't acknowledge that, MY head canon is truth'
So this chibi that I drew, I was attacked by NES/GB purists(or just one guy pretending to be a few) who hate a more androgynous looking or cute Pit. I was told I should take down the chibi from my tumblr and be ashamed I called myself a Kid Icarus fan for even ever liking any aspect of Uprising.