I understand your concern with the upped brightness of the graphics in terms of atmosphere. If there's one place in the game I'm most concerned about, it's the forest temple. I thought the layer of darkness that enshrouded the temple enhanced the atmosphere to a level of unparalleled perfection. I'm worried that brightening the temple might break the spell that the darkened atmosphere places on those that enter its confines.
Basically, my concern for this first arose when I saw these screen shots:
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However, I had been thinking before that they may still lower the darkness to a more suitable level before the final game is released, meaning your worries and mine would be unfounded. Taking a look at a more recent screenshot of the forest temple, I believe they have indeed done exactly this:
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See that? That looks like the correct brightness and atmosphere to me. Likewise, I'm thinking there's no need to be worrying that other places in the game where the color balance is a key component of the atmosphere (i.e. the shadow temple) will be ruined in any way.
All in all though, I think we should all reserve judgment until we play it ourselves, as we will not know how the brightness is exactly, as well as how it will affect our experience until we have gone through it first hand.
That being said, this concern arises only in portions of the game that are meant to have a dimmer level of brightness in relation to the atmosphere. In terms of the color found throughout the overworld however, I think it looks absolutely brilliant, truly working to bring out Hyrule and every one if it's charms, presenting it as the vivid, rich and lively world it was meant to be.
Take a look at these comparative shots. Can you really not be satisfied with the color in the 3DS version featured on the right? I think it looks magnificent.
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Looking at the last few screenshots actually, there is one more thing I think you should keep in mind. The colors are not going to be bright all the time; remember that the lighting will change throughout the day. Take a look at this:
The coloring looks rather more like what would be found in Twilight Princess, wouldn't you say? It is in part due to the time, and in part due to the location. Do not think that the colors will hold a static saturation level throughout the entire game. I believe the colors will change accordingly depending on appropriate factors (time, place) contingent to the situation, and I am inclined to think that when you actually see this for yourself game in hand, you will be quite satisfied with the experience that the graphics give you.
That's just my two cents. (Or maybe it's two dollars worth looking at the length of this post >_>)