To solve your graphics inconsistency problems I recommend keeping the saturation levels for all objects on a given 'plane' the same. For example, if you have three "layers" (background, middle ground, and a foreground) then all objects in the background should have the same saturation (which should be a mid to low saturation value), all objects on the middle ground should have the same saturation (their values should be noticeably higher than the background's), and all objects on the foreground should have the same saturation values (which should be noticeably higher than the middle ground).
The base value (i.e. the background's saturation) should depend on what mood you are trying to invoke. A high base saturation gives you a more vibrant cartoon-like feel while a really low base value will give you a more grim, dirty feel. You should always leave a little room on the top layer's value (try not to exceed 95 for the top layer) so that your special effects can have the highest value over all, which will make them "pop out" better.
Where the brightness is concerned, try to keep stuff in the background fairly mid-range (not too dark and not too light), reserve your brightest and darkest for the upper layers. Anyways, to give you an idea of how this all works I whipped up the following:
EDIT: If you're wondering why things in the background have less saturation it is because dust in the atmosphere washes out the color. The further things are from you the more dust in the air you see between them and thus they appear less colorful.
As such, the greater the difference between the saturation value of two layers/planes the farther apart they'll appear. Your layers will have a greater difference in a valley setting (where there is a lot of open space) than in a house (where walls are fairly close together), for example. The effect can be enhanced by having lower layers be tinted by the sky (for example, if your sky is blue then the lowest layer will have strong blue tinting but progressive layers will have less and less of that blue tinting). All that dust reflects the color of the sky, so not only does it wash out the colors of things in the distance it also causes them to pick the color of the sky. Fog or dust clouds (etc.) can also cause a similar in confined spaces by reflecting nearby or ambient lights (or lack thereof).
(The little squares are SAT:100/BRIGHT:100)
Notice how the second is a little less painful to the eyes, lol.
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