To be fair the good Zelda games never did this either. In fact I'd say it wasn't really til that spinning top thing came along in TP that anyone even had this complaint about Zelda. If we go back to the 3D debut, Ocarina of Time, almost everything you got would be used again in subsequent dungeons. In a sense, the Child Link items "upgrade" (slingshot replaced by bow, hookshot succeeding boomerang).
Those items upgrade further too. Adding fire arrows that burn webs or ice arrows that create platforms are not far off getting explosive arrows in Tomb Raider. Similarly you turn your hookshot into the longshot and in a sense even upgrade your boots and tunics to have different attributes.
I'm not saying you don't have a point, but I think Nintendo already know that they've made mistakes on this in the past, that's why SS took a new approach to shields and pouches, and ALBW came up with a whole new system for dungeon-dependent gear.