Crystalis (NES, 1990)

Before talking about Crystalis (1990) for the NES, I'd like to briefly discuss Zelda II: The Adventure of Link which came out around the same time.  As a sequel to The Legend of Zelda, I think it fails pretty drastically.  This is not because it is completely different from its predecessor, but because the new things it tries are executed poorly.  The top down gameplay of the first game is abandoned (except for on the map screen where you cannot fight) in favor of traditional side-scrolling platforming.  Also introduced is an experience system where you level up for fighting enemies.  This game has aged quite poorly.  The control is slippery and lags a bit, the level design is sadistic at times, and the experience system encourages more grinding than in Dragon Warrior.
Having said that, here is Crystalis, a top-down (a la Zelda) action-RPG that in my mind, very well should have been Zelda II.  The story is about a nuclear war that ravaged the world some centuries ago, and your character awakens from a cryo-sleep chamber with no memory of anything.  He awakes to find that the empire of Draygonia is trying to use an ancient power sealed away on a floating island to take over the world.  It may not sound like much, but for the days of the NES, it is practically Shakespeare.
In terms of gameplay, it basically does right everything that Zelda II did wrong.  You have an overhead view of the action, allowing more precise swordplay and dodging maneuvers.  You upgrade your character stats with every level, and levels increase by collecting so much experience.  Grinding is actually handled very well in this game, as enemies give reasonable amounts of experience for killing them, fights don't take very long, and enemies respawn.  This all makes farming for experience fast and painless.
Apart from being successful in standard RPG elements, Crystalis also has its own unique innovations.  By holding the attack button, you can charge up a beam that will fire from the sword, allowing you to attack enemies at a distance.  Combine a sword with special items and you can get a bigger charge.  Larger charges are more powerful, but at a cost of taking longer to fire.  There is a nice strategy to it.  You collect four elemental swords, and different enemies are vulnerable to different elements.  There is also a system for different magic spells, some used for battle, and some used for context-sensitive situations.  One spell allows you to disguise yourself, which can be used to breach enemy security.  Another lets you put a person to sleep.
Crystalis has some of the best looking graphics on the NES.  Character sprites are well-drawn, and backgrounds and environments are colorful and detailed.  In addition, the music is lively, fits the mood of each area, and is fairly memorable.  There were many underrated games on the NES, some of those including The Guardian Legend, Journey to Silius, and Metal Storm, but for my money, Crystalis is the best of them.  It is an epic quest that was criminally overlooked both in its day, and today.