Allow me to take you on a journey back in time.
There are 3 games that have been slightly mentioned in this thread, and only one of which was named.
NES: Solstice. Incredibly deep puzzle solving, amazing soundtrack and fun items and abilities
SNES: Secret of Evermore. Lots of weapons, charge attacks, summons, spells, alchemy, free roam gameplay, robots, dinosaurs, bazooka's, time travel, swords, spears, Hidden items, a perma sidekick who changes shape and abilities based on where you are. Tough boss fights, space ships... I could keep going! This game is overlooked so often that it's sickening...
SNES: Illusion of Gaia. This game has one of the most incredible storylines i have ever experienced. Genuine character growth, hidden item collecting, shapeshifting, ability upgrades, and this is in the first hour or so. It deals with loneliness, loss, slavery, and the death of an entire civilization waiting for someone to show up. ITs... Go play this game, right now!