As requested I have read back to the beginning of posts by Mark, Chris, and HD. Go back far enough and you find Mark and HD disagreeing about the nature of ukemi. Now it seems that Mark is a convert.
From the beginning HD has been arguing that Aikido practitioners don't know how to defend themselves and that, though he doesn't train Aikido, that he knows true Aikido. Without clearer language and description it will be difficult to determine the extent to which what he is doing is Aikido, or some other art, or to judge his understanding of Aikido. We do find hints, however, that suggest a lack of understanding of the basic conception of Aikido. For examples, in one post he argues with Mark about why you would ever chose to fall down in response to a strike while in another post he argues that high ranking Aikido practitioners are unable to put him into locks or otherwise do Aikido to him.
Aikido is not based on the ability to "do" anything to an attacker. This is a basic misunderstanding of how the art works to think that anyone can put a lock on you if you aren't really attacking or that a given attack would lend itself to a lock (or even a particular technique). In fact O'Sensei was very clear on Aikido not being about technique at higher levels. O'Sensei was very clear that Aikido works in response to the attack and that the attacker is at a disadvantage for having broken the harmony of the universe. Chris might quibble over the translation of a word here or there, but the meaning is not lost. If we take the following quote from an interview with O'Sensei (which is less likely to involve translation problems than written work) we see O'Sensei making this point:
“In aikido, there is absolutely no attack. To attack means that the spirit has already lost. We adhere to the principle of absolute non-resistance, that is to say, we do not oppose the attacker. Thus, there is no opponent in aikido. The victory in aikido is masakatsu agatsu (correct victory, self-victory); since you win over everything in accordance with the mission of heaven, you possess absolute strength" (1976).
I think it's fine for HD, Chris, and Mark to question O'Sensei's ideas. But in doing so they should first acknowledge what his ideas were. Though more clarity is needed to make a final determination, it seems that they are describing an approach to the martial arts, that while potentially very good and even complimentary to Aikido at times, is not Aikido. HD's project seems to be to basically argue that O'Sensei had not developed a new art, that modern practitioners of Aikido don't understand what he was doing, so come pay me to learn how to do real Aikido. It is a mistake to take Aikido into the realm of fighting. Aikido is not about fighting. Aikido is not well suited for competitions. Aikido is about the refusal to fight. This can take many forms. The taking of many forms (including breaking balance internally and externally), spontaneously responding to a dynamic situation in an attack, is the meaning of Take Muso Aiki.
The cooperative nature of Aikido training is part of the "system" of teaching Aikido that O'Sensei developed (see Saotome Sensei's books). So, to answer the question HD asked years ago, Uke chooses to fall down in response to the atemi of Nage, so that Nage can learn to move in such a manner as to elicit that response more of the time. Uke also falls down for the same reason that boxers fall down when struck hard. Now imagine a boxer being struck and tripped at the same time as he came in and tried to punch himself. That's what Kokyu Tanden Ho basically accomplishes. There are problems in Aikido, in my opinion, but these problems are not those described by HD, Chris, and Mark. A problem in Aikido is that the system that O'Sensei developed has too often been forgotten. Another problem is that people try to make Aikido something it cannot be. Aikido can never be a cage fight art. There may be Aiki in arts like MMA. But that doesn't make them Aikido. I would argue that Aikido is closer to pure Aiki, as O'Sensei believed, but that doesn't really matter to this discussion. This discussion is supposed to be about Ueshiba's Aiki. He said his Aiki was based on leaving this plane of existence in order to engage in absolute non-resistance.