Really, we don;t even need to look to other games, rather, take a fresh look at the series, without the learned "expertism" that we all carry, taking things at face value. Look at Zelda with fresh eyes and I think we would all be amazed at what we find, location-wise.
The shadow temple in OoT was a torture camp utilized by the Sheikah during the Hylian civil war, the Deku Tree is a guardian spirit that happens to have a hollow inside filled with partitioned rooms and functioning doors.
Just take a step back and look past what we consider old hat.