I decided to post this on the weekend because it's too short of a thought for a full article, but the theory is interesting so I thought I'd share.
It's clear to me that the Grey Knights codex is made of up pretty darn powerful individual units, even when you take their high costs into consideration. It's equally clear to me that there is a lot of synergy missing from the codex, which is a hugely limiting factor which keeps the codex from being absolutely nuts.
For example, the HQ you'd love to take in most GK armies, a Librarian, has terminator armor which means that he can't be put in the units you'd want him with, namely MSU guys in Razorbacks. So a list with the best possible troops can't have the best possible HQ without some awkward, non-synergistic changes. Another great example would be Crowe. He cannot join a unit, so the most obvious build in the codex, MSU Purifiers suffers from his awfully awkward HQ choice.
On the other hand, some codices are nothing but synergy. IG and Dark Eldar jump out to me as the 'dexes where raw power is least, but due to special rules and the ease of army construction, the armies are often greater than the sum of their individual parts.
In other competitive strategy games this conflict between synergy and power ebbs and flows. Sometimes the tools are there for synergy to trump power, other times it is reversed. While your mileage may vary, my experience in this game and others tells me that Power trumps Synergy when they are around equal to each other.
Do allies change that? I'm not sure. Allies can create insane synergy. Allies can also provide very awkward additions that have no synergy but have tons of power. I'm anxious to see how NOVA goes to give some insight as to which way the wind is blowing.