Is not that militia weapons are not protected. They are. It's just that the definition of those protected militia weapons has been watered down. From Silberman's decision:
"We take the outfitting requirements of the second Militia Act to list precisely those weapons that would have satisfied the two prongs of the Miller arms test. They bore a “reasonable relationship to the preservation or efficiency of a well regulated militia,” because they were the very arms needed for militia service. And by the terms of the Act, they were to be personally owned and “of the kind in common use at the time.”
Well, this was fine in 1792 -- personal weapons were militia weapons. For the most part, they were indistinguishable.
Today, however, arms which bear a “reasonable relationship to the preservation or efficiency of a well regulated militia” and arms that are "of the kind in common use” are, for all intents and purposes, mutually exclusive.
If future courts are going to submit arms to this Miller "two-prong" test, it will severely, and I mean severely, limit the arms that would apply. Just given the limited practicality (and high price) of some militia-suitable weapons (eg., a .50 bmg rifle), it won't be "in common civilian use" and therefore not protected.
Unless the court changes the definition of "common use" to "in common use by the average militia member (military soldier)", we are royally screwed. Granted, this list would include a weapon like the M249 SAW, but reasonable regulations could handle those cases. As it looks like now, the M249 is not even protected. As weapons become more sophisticated, the civilian "militia" will fall further and further behind the federal standing army -- just the opposite of what the Founders intended.
The one statement that troubles me from the Parker decision was to the effect that the word "arms" is so indefinite that it must look to the prefatory language for its definition. Given that the protected common-law right includes self-defense, then "arms" must also include items which are particularly suited to self-defense.
Your concern regarding "in common use", I think, is not a great concern.
The Parker court was required to address the objections of DC to the effect that Miller applied. Since it was possible to establish, through the requirements of early militia laws that pistols were required of a subset of the militia, then one must presume that the pistols were in common use at that time, and the court reasonably included the lineal descendants as qualifying under Miller. The Parker court made no further attempt to determine whether "common use" or "linal descendancy" were absolute requirements. Whether a machine gun is a lineal descendant of a rifle is of little concern, since no Court would ever claim that a state-armed militia could not have them.
This discussion of "common use" and usefulness to a militia is aimed squarely at not having to attack Miller, while still recognizing Heller's protected right.
In keeping with the Supreme Court's desire to make a narrow ruling, I would expect that they can afford to say little about whether the holding in Miller must be addressed. Only the fact that Miller and Layton didn't have to be members of a militia needs to be addressed. The scope of "arms", which clearly includes pistols, need not be further addressed by the Heller Court.
Ginsberg can be lulled back to sleep and provided a little cover by the claim that "in common use" can be used to prohibit arms suitable to a militia. But I think she knows better.