Okay, first of all, we need to set things straight. Skimmers DO NOT directly remove nitrates and phosphates, so to argue that skimmers are proven good because they remove these compounds isnt a valid argument... its wrong. If Randy's article is what you want to go by here, then you will see he even says the same thing. The basis of the idea that skimmers arent proven is that if a protein skimmer is taken off of a reef, there are still plenty of other mechanisms in the tank to deal with nitrate and phosphate... because they are there in the first place dealing with all of the other phosphates and nitrates your tank produces.
AND, although high levels of phosphates and nitrates are bad for all inverts (except some like clams), trace levels are used as nutrients. Heck, you know this, even copper is used as a trace element. Removing a skimmer from a system does not mean that your phosphate and nitrate levels are going to rise, as is proven by all those reefs out there that are running without a skimmer.
Now, the argument that has been brought up by the likes of Schimek, Bornemann, Riddle, etc. is that the proteins that we remove would otherwise be consumed by the fauna in the tank... recycled into the eco-system. These proteins are NOT nitrates and phosphates (they may contain them, or break down into them to some degree, but they are not equal to phosphates and nitrates themselves). Randy explained that there are many other proteins that a skimmer cant get out, but that they arent that bad anyways because they get consumed by the bacteria in the tank. What, you think that these bacteria wont eat the rest as well?
So cite all of the articles you want on how phosphates and nitrates are bad for corals, I dont disagree with you, but what you are saying that A+B=P, when that is just not true.
Here: Ill put the burden of proof on you this time. Show me something that proves that protein skimmers are the only way that a reef aquarium can deal with nitrates and phosphates.
Randy says "On the other hand, skimming almost certainly removes many micro- and even macroorganisms from the water column that might otherwise become food for a tank's inhabitants (as well as the organic molecules that might be food - like proteins). It is not clear how large an impact this has, but it certainly depends upon the type of inhabitant that is being considered and the skimmer's efficiency."
Also "Most highly polar organics will not be removed by skimming. Simple sugars, acetate, oxalate, methyl alcohol, choline, citrate, etc. will remain behind. They simply are not sufficiently attracted to an air water interface. Most charged species are, in fact, repelled from the air/water interface, so they are not collected. Fortunately, many of these highly polar organic materials are readily metabolized by bacteria and other organisms, so they do not continually build up in marine aquaria."
And "In general, nitrite, nitrate and phosphate will not be directly skimmed out of seawater because they do not adsorb onto air water interfaces."