I have been asking myself this question....and I think they have, but that was probably in the first update that they made the colors more subtle.
It also depends what screen I'm looking at. If I look at my iPad mini (original, does not have retina display) the color of...let's say the messages app, is not that bright. When I look at my iPod touch (5th gen, has retina display) the greens are definitely brighter and scream 'look at me'. When I look at my iPhone 4 (has retina display) the greens and other colors are halfway between how they look on my iPad and how they look on my iPod touch.
I guess it's a thing of displays and their variations. I don't think too much of it.
-Juan