The main play mechanic centers around magical gems (original, I know) that "bond" with pieces of the hero's equipment and give them magical powers. It's partly inspired by the Materia system from Final Fantasy Whatevernumberitwas, and the tunics and boots from Ocarina of Time. Each piece of equipment has "slots" that power gems can be assigned to (number of slots is a property of the item, along with other qualities like attack strength, defense, etc.), and a single gem can be assigned to multiple pieces of equipment at a time (depending on the power of the gem, which can be raised with experience). The "bonds" between gems and pieces of equipment can be changed on the fly.
The gems represent the four elements, plus light, shadow, lightning, and nature; the elements oppose each other in the usual way, light and shadow are opposed, and lightning and nature oppose themselves. The pieces of equipment they can bond with are the helm (sensory and mental abilities), breastplate (resistance to environmental effects), gauntlets (touch and lifting), boots (are made for walking), shield (defense), sword (sword attacks), and the secondary weapons (bow & arrows, magic staves, etc.). For example, bonding the shadow gem to the helm allows the hero to see through illusions (which are light-based), while bonding the light gem to the helm allows him to see in the dark. The earth gem when bonded to the boots aids in traction, the water gem allows you to walk on water, the air gem lengthens your jump and cushions falls, etc.
Part of the idea is that the gem you start out with in the beginning of the game is either randomly determined or chosen, and that to a certain extent determines the order of the main dungeons (at least for the first part of the game). I've always liked the Mega Man system, where you can attempt the stages in any order, but the powerup you get in one stage makes another stage easier.
alun_clewe's recent posts on logic mazes have also prompted me to think about how puzzles should work. What I'd really like to see is randomly generated (but provably solvable) puzzles and mazes. The problem with preset puzzles is that they're no longer puzzles as soon as somebody writes up a walkthrough on GameFAQs; they're just tasks. Dynamic puzzles would fix that problem, and would also contribute replay value.