I thought I was going to be novel by proposing Crystalis. But it turns out someone already said it! I loved that old game much more than the original Zeldas. The gameplay, abilities, and storyline all melded together in a harmonious way that few current adventures can.
Chrono trigger for SNES (and its pending re-release to DS) is also a great companion to the Zelda series, mixing action oriented gameplay, rich storyline, great character design, and a very cool plot that has tons of replay value.