Zelda was never suppose to be a linear franchise like Uncharted. It started off and sold due to its non-linearity mixed with RPG qualities inspite of being an adventure game.
Asking for natural plot progression in Zelda will kill it. Maybe Uncharted can get away with that, maybe Half-Life can get away with that, but games such as Zelda and Metroid cannot get away with that. They were not born as linear story games. Your friend is wrong because he expects from Zelda the kinds of things he expects from games like Uncharted, but expecting the same exact thing from a completely different series is like wanting the franchise to kill itself.
By the way, TLoZ for NES isn't the only non-linear Zelda game TC. ALttP and OoT fit in that category as well.
