It's rather a simple suggestion: adjusting the transparency values for layers. For example, 85% transparency allows to barely see an object behind another object you can clearly see, but the object you barely can see can be picked up by Link. Catch my drift?

Secondly, it's probably possible by script(and suggested a few other times), but a "Link/NPC Reflection" and "Reflective Water" combo would be nice to have when you want to have a more realistic experience. It would look pretty cool, also.