Ocarina of Time 3D is probably my pick. It took the amazing foundation that was the N64 game, and fixed most (if not all) of the clunky old-fashioned mechanics of the original. Making Iron Boots into a C-item and giving the Ocarina a dedicated button turned the Water Temple from a tedious mess into a pretty good dungeon.
Fire Emblem Echoes was a superb game, though I've never played Gaiden as a reference. It seems like the upgrade was pretty significant though.
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