In “Trial run” you assert that the Bush Administration has decided to use civilian courts where they have good evidence, and POW status and/or military courts where they do not. But of course, you do not know what evidence they have in the military cases, or even in most of the civilian cases, the trials not having been concluded, and Lindh having plead guilty.
You also assume that it is easier or more fair for the defendants if they are tried in civilian courts. This is certainly true insofar as rules of evidence are concerned, but not necessarily in terms of outcome or length of imprisonment. I understand that Lindh will serve 17 to 20 years, which may well be more than any of the POWs will serve (impossible to know, of course).
You have overlooked another possible rule that the Bush Administration could be using, which also fits the facts and a reasonable understanding of what an “enemy combatant” is, as distinct from someone who is aiding the enemy. In cases where the defendant is caught in the Middle East, or immediately upon arrival from the Middle East, he will be treated as an enemy combatant, a prisoner of war. No trial is needed, but punishment is limited to imprisonment for the duration of the conflict (which may be a long time, certainly, and the end will probably be determined by a future President, not Bush).
The only exception to this rule is the case of Lindh. But despite your assertion that “there does not even seem to be a trend over time. Some legal scholars who defend the administration had predicted that it would increasingly avoid civilian courts as the war on terrorism progressed,” his sole exception to the above rule probably is related to the fact that he was arrested earliest, when the trial policies were being worked out, and as I stated above, the fact that he was a citizen and facing a civilian trial, leading to his plea agreement, did not give him any advantage over the POWs, and also got him to agree to cooperate with the U.S. (you and I do not, of course, know how helpful he is).
Finally, the fact that U.S. citizens are not subject to military tribunals is in fact a concession even though some are getting no trials at all. As POWs they are only subject to imprisonment – albeit for unstated terms – while the only real purpose of a military tribunal would be to get a death penalty for war crimes.
Second, there are mechanisms for an American to lose his citizenship, and they're spelled out in every American passport. However, the wording say may lose citizenship. That means that someone looks at the case, and decides whether the schmuck is still a citizen or not.
Since passports come under the authority of the State Department, it's an executive function. There may be some obscure law that dictates how this citizenship board functions. Or maybe there isn't. Perhaps it's done under the department's general grant of authority to organize itself, just like it organizes the summer picnic committee.
In either case, if determination of citizenship was within the purview of the judicial branch, we would have heard of it already. That means the final decision on someone's status rests solely in the hands of the executive.
To prevent this from being arbitrary and capricious, one has to leave the US first, and then participate in the activities mentioned on the passport. When captured, someone in the DOJ will determine whether they still consider you a citizen, or an enemy combatant.
Personally, all of the clowns they're treating to a regular court trial seem like enemy combatants who do not conform to the Geneva Convention to me, and should just be disappeared into some black hole. But for whatever reason, they're being treated as citizens, although a bit wayward in what they did. I don't know why the government is doing it that way, but it sure seems legal and constitutional, even if it seems to be a tactical mistake.