"As for myself, I would never consider juxtaposing inner movements in a symphony by Brahms, Beethoven, Rachmaninoff, Shostakovich, whomever".
That's because none of those composers has a situation that's even remotely similar to that of the sixth Mahler - if not biographically, then at least musically speaking. If that weren't true, how could it have been possible for there to exist, three or four decades worth of M6 recordings in which the vast majority of them were in S/A order, with nobody being the wiser? The vast majority of people who purchased those recordings probably weren't aware that there had ever been any controversy surrounding the inner movement order. And even among those who read the program notes far enough to discover that there had been some question, probably didn't consider it to be very important - or just couldn't care. Obviously, there are those who took it up as a cause long ago. But that's undoubtedly a very small percentage of listeners.
"So, if a conductor maps out his route through a work as complex and emotionally intense as the 6th, wouldn't he think through tempi, transitions, and the emphases in such a way that the order of movements establish flow? And what effect does it then have on the integrity of the performance to juxtapose movements? This is a different issue from the question of the order in which the movements are performed. If a performance is in S/A order, it has (or should have to my mind) a sense of coherence based on the fidelity to that order. It has an integrity as a work as a whole".
In my opinion, this is assigning too much importance to the role of the conductor. But more to the point, when I express my preferences on movement order - based upon extreme tempi chosen by the conductor, etc. - I'm not stating that preference as a truth that should be applied to other people. I'm only stating that which "works" and, "doesn't work", for me. A good example of this is the MTT/SFSO M6 - a recording which, to my mind, just doesn't work as a large conception. When I listen to it again in A/S order, I find that it works much better - for me. As I mentioned, MTT DID switch to A/S order when he performed M6 in L.A. I'll bet anything that he didn't significantly alter his tempi and tempo relationships when he conducted it in L.A.
If, what you say, Amphissa, were a musical truth that must be applied to the Mahler sixth at all times, then MTT should be barred from switching the inner order himself, unless he proves to the Mahler P.C. Board that he has sufficiently adjusted his tempi and tempo relationships in accordance to such a truth. Therefore, what's good for the goose, is for the gander. If it's OK for MTT to get up in the front of the LAPO and switch the inner movements (back to where they allegedly should have been all along), then surely it's OK for me to be doing that in the privacy of my own home, right? (and don't call me Shirley). That's just good, old logic - if A, then B.
"And wondering if the reason is because it really is a significantly flawed work, lacking a sense of coherence and unity, as evidenced by the fact that people can just shuffle movements without destroying the piece"
A-ha!!! - here's the crux of your argument, and what you've been trying to get at all along. I think you're going to be surprised by what I have to say on this: to some degree, I think you're right. I've always made the argument that if you took away the scherzo altogether, you'd have one of history's greatest three movement symphonies. In a sense, the scherzo is superfluous. It fits on either side of the slow movement, yet it's somewhat unnecessary. Your argument has always been that Mahler does too much marching in the first movement. Since I view the sixth Mahler to be something of a protest work, I find that marching music - in minor, which is unusual for marches to begin with - to be central to the work's overall narrative. But more to the point, it's simply the nature of that movement; either one can live with it, or they can't. I can't imagine that fans of baroque music, for instance, could suddenly relate to Mahler six (and I hate most baroque music, in turn). All of this doesn't mean that I want to see the scherzo go away. But what I do think it means, is that a strong performance of the scherzo is key, regardless of where you put it.
One of the greatest arguments about putting the scherzo next to the first movement, is that it can sometimes sound like you're starting the symphony all over again. To some degree, that's true. Furthermore, the conductor needs to consider the following when performing M6 in S/A order: should the scherzo begin at the same tempo as the start of the symphony (Gielen); the same tempo as the end of the first movement (which in a sense, will sound twice as slow because the timpani are playing eighth notes at end of the first movement), or some tempo that's split right down the middle of the two (Boulez/VPO)? Anyway, this has been a point used by those who insist on A/S order. In my opinion, those people fail to see another problem, which is that the last 120 seconds of the scherzo - starting somewhere before the tam-tam smash - behaves in almost identical fashion to the last few minutes of the finale; starting before the spot where the third hammerstroke was originally located. Both cases are in A-minor, no less! In a sense, the scherzo combines the march music of the first movement (but in 3/4 time), with the dissolution and collapse of our "protagonist" that happens in the finale. From a purely musical standpoint, one problem with the scherzo is that the number of minutes taken up by Trio type music (slower) is actually far great than that of the various scherzo (faster) variants. The scherzo is a tough case, because there needs to be a sufficient tempo contrast between the scherzo portions, and the various trio sections. Yet, those trio sections shouldn't drag (go too slow). Yet, the scherzo is written in a way that can only go so fast. Gielen solves this problem by doing the scherzo at a tempo that's identical to his M6 beginning - which is slow to begin with - and then almost unifying his tempi across the scherzo movement. In other words, minimizing contrast between scherzo and trio sections.
Putting the scherzo after the first movement makes for a fully unified Part 1; comprised of the first two movements. Granted, this makes for 35 to 37 minutes of music that's predominently in A-minor (one argument for leaving out the exposition repeat? - and I wonder how much of the finale actually stays in A-minor?). Furthermore, the beginning of the finale is far more shocking when it follows the Eb Major resolution of the slow movement. The start of the finale is more or less in C, and then settles into A-minor by the time it gets to the tuba solo. I can't help but think that if Mahler had truly first conceived of his sixth symphony as a "classical" A/S one, he would have also composed the scherzo in a different key - possibly D or E minor. At some point - probably at the beginning - he must have thought of the scherzo as a commentary or extention of the first movement; one in which the "happy" ending of the first movement gets negated by a collapse that's almost identical - in nature - to the sort of collapse and disillusionment that happens in the finale. Question is, was that necessary, or could he have simply segued into the remote highlands of the slow movement (in Eb Major), and then left the scherzo out altogether?