The published syllabus of U.S. v. Miller, which was prepared by a court reporter and has no legal weight, does not accurately reflect what the decision actually says. Unfortunately, at least one lower court based a decision upon the syllabus rather than the case itself, and some other courts have based their decisions upon that one. No matter how many decisions are written based upon a faulty reading of Miller, that won't make such a reading correct.
The Supreme Court ruled that the government could proceed with its case against Miller's co-defendant Frank Layton. The government declined. Are there any other cases you can think of where the government has scored a "victory" and reacted by offering a plea-bargain?
Had Layton's case gone to trial, he would have been allowed to introduce evidence that his shotgun was indeed an instrument suitable for use in a well-functioning citizen army. Given that the U.S. Army had in fact used such weapons a couple decades earlier, such evidence would have led to his acquittal.
The syllabus in Miller not leaves out some of the critical surrounding circumstances (e.g. the reason there was no evidence for military utility was not that Miller/Layton had failed to provide any at trial, but rather that their trial hadn't even happened yet and thus they'd not been allowed to present any evidence of anything). Further, it alters some of the Court's wording so as to change its meaning. The Court said there was no evidence before it that a sawed-off shotgun was a militarily-useful instrument; the syllabus changed this to state there was no evidence that Miller's possession of a sawed-off shotgun would serve a military purpose.
An honest reading of Miller would indicate that the Second Amendment protects personal ownership of weapons which have military utility, but that--in at least some cases--the burden of proof could be placed on the individual possessing a weapon to demonstrate of its military utility.
That other courts have chosen to cite the syllabus rather than the decision itself, or to cite other court decisions which in turn have done so, is sound reason to consider those courts to all be in error.
That is about all we can take from what the U.S. Supreme Court said in Miller. All the rest is conjecture.
Since Miller, all the lower federal courts (save the 5th) have ruled that the Second Amendment protects personal ownership of weapons (which have military utility) as part of a militia.
Furthermore, an honest reading of Miller would allow the personal ownership of weapons far more lethal than sawed-off shotguns. Since we no longer have the citizen militia as envisioned by the Founders, how are we to implement this "honest reading"? M203's for everyone?