I would like to start by saying that I like the idea very much and I applaude the EO staff for having a good idea and the imagination and creativity to try making it work.
The question has been raised as to how the armies would work together and why they would in the first place. Well, I actually have a thought to share on that. ALL Eldar, remember a time before the Fall when they were the true Masters of the Universe. (no relation to He-man) A time when the race as a whole was strong, the culture was rich (not monetarily) and their actions had great meaning beyond that of mere survival, which is the case now. Even people wrapped up in their own schemes and plots will long for a time when things were better, and no matter how twisted they are, they will strive in some way to better themselves even if their perspective and means to an end is slightly warped.
People have talked about the arrogence, selfishness and twisted depravity of the different races, which is what was the races near destruction. None of those things equate to stupidity though, although they may be contributing factors at times.
That being said, it stands to reason that the various leaders will participate in this adventure as a means to an end, be it the greater good of the race and/or their own greater good.
The Farseer is wise and very knowledgable. (let's assume ok? overlook the haughty arrogance for a sec.) Knowing his history and the impending fate of the Eldar, he could be willing to look to the abilities and advantages of the whole race to find a way to prevent it. He knows there is strength in numbers as well, (something CWE, DE and Harlies lack standing alone) and that there are vast and experienced resources that can be tapped into, ie. Harlies and DE, that can bring something to the table that he and his CWE lack. He remembers the most what it was like before the Fall, as everywhere he looks is a reminder, and would have the strongest desire to keep what he has, even if it means overlooking what he does not like about his cousins.
The Archon is intelligent, cunning and shrewd. (abiet twisted and evil which do not always equate to insane) Generally his is a thirst for power, (of many kinds) and working with his his delusional cousins may be the way he sees to be the dominate power in the universe again and his way to achieve the piece of that very large pie. He also operates on a survival instinct. No Archon, or any DE is in a rush to die, and uniting with CWE and Harlies may be the way he sees to perserve his life for a little longer.
Harlies, well they are the middle ground. (and can be argured to have the arrogance and insanity of both races, but we will again overlook that) And to date the only Eldar who operate between all of the different worlds of the Eldar. He may recognize his cousins faults and idiosyncrasies for what they are, but sees past them to the Eldar who wields them. The dance they practice is a representation of history and art imitating life the way it was. Their goal could be to change it so they are no longer imitating it, but living life as it is meant to be in their eyes. He does not operate on a self survival instinct, but a race one.
In the end it burns down to preservation, self and race. Hatred, animosity and distrust will and do exsist, but they can be used as a tool when coupled with the aformentioned motives. They can also be used as careful, but tenuous, building blocks.
No society is perfect, and all have their struggles, but they always seem to manage to survive. Or they end in flames. But there are those brave enough to try and make it work for whatever reasons, like the Eldar of this Craftworld.
That was the 'WHY', and here is a possible 'HOW'.
A possible way to achieve balance on the battlefield would be to have more than one HQ. In large enough battles, (at least 2000 pts or more) an HQ representative of each faction would be present, in smaller battles, (2000 pts or less) make it only two. Be it a Farseer and an Archon, Great Harlequin and a Farseer and so on....
Using the full organizational chart, the breakdown could be easy. You have 6 troop choices, which could be divided into 2 apiece. 2 DE warriors, 2 Guardians, and 2 Harlequin or Mime Troupes.
The same goes for the Elites, Heavy Support and so on, which each have three choices to fill, that can't be divded completely even because Harlies lack in some areas here. But if a player takes 2 Falcon Grav Tanks in his/her Heavy Support, then his 3rd choice would have to be DE, and the reverse would be the same.
A balance would be possibly in Fast Attack were he/she would have to take 2 Reaver squads, and 1 Shining Spears. (just exaples)
In smaller games the breakdown is a little more difficult as you don't have as many slots to fill. If a player took all 4 troop choices of DE warriors, then his/her Elites and Fast Attack (and so on...) could not be occupied by DE.
But it would provide a balance so that all armies are represented. It could be made so that only 2 of the 4 could be dominated by one race. An example would be 2 squads of Guardians, with 1 of DE warriors, and 1 Mime Troupe. As long as no one choice is totally dominated by a paticular faction.
Another option could be that if a player, for example, took an Archon, (as 1 HQ choice) he could take all his troop choices as ONLY DE warriors, but the rest of the army would be made up of ONLY Harlies and CWE.
These thoughts though are for the smaller games and rules could easily be set up for organizational charts for small armies with variations of different HQ's.
Ok, now that I have been really long winded, I will shut up. Agree or disagree, I hope that my imput was helpful, or at least moderately amusing.
And if anyone in the powers that be at EO thought anything I said was worth while, I would be more than happy to help in any way that you need me.