Ocarina of 3D cannot bring the same feeling because our perception changes with our age, especially if Ocarina of Time was of the first games you played or one core in your childhood. I have found out that as a kid I filled many gaps and I didn't know what to expect, now for the remake I can have expectations than when not meet end in disappointment.
Ocarina of Time didn't disappoint me and allowed me again to rediscover Hyrule, it was like visiting back after a long trip away. The place looks almost the same but you can tell apart what is different because your memory is so vividly. The details they did to enrich the looks of rooms and stuff in OoT 3D were appreciated but now the game seems too simple by today standards.
That aside I understand your concern for the feeling, because I share it. If the moon is something to speak for, it seems to keep the dark Aura, however Mr. Iwata mentioned about making the game available for everyone, which I have in the past seen to mean downgrade somethings, I am not sure if that will happen in MM.
So far it seems to be trying to keep things like they were, which I commend, but we have only see few snippets. It's great they have finally come to the open regarding the remake.