I'm only going to point out one issue which has not yet been mentioned in this thread, and that has to do with DOC, dissolved organic carbon.
"Carbon" as in activated carbon in filters removes many substances from the water, and depending upon the amount of whatever is being removed, the carbon does "give out," and at that point has been shown to release toxins back into the aquarium. Others have talked about this, so I will move on to DOC.
DOC is one thing carbon removes, and this is rather ironic, because DOC can do the job of the carbon better. To define DOC:
Dissolved organic carbon (DOC) is a general description of the organic material dissolved in water. Organic carbon occurs as the result of decomposition of plant or animal material.
This is why we leave the substrate alone in planted tanks; we want the organics to be broken down (by snails, then bacteria) so it forms DOC. Not only is DOC an essential source of CO2 for plants; it also offers the greatest protection against metal toxicity in natural waters, and in the aquarium. Metals readily bind to DOC. By removing DOC, the filter carbon is thus removing minerals that are essential to plants and also to fish to some extent.
As the fore-going should suggest, using carbon in non-planted tanks may not be so wise either. It all depends upon the state of the biology and water.