A used copy of the Abbado/BPO M6 came in at work, so I decided to give it a revisit in a "neutral" location (at work, as opposed to at home). Regardless of the current "p.c." climate of performing M6 in andante/scherzo order, I strongly believe that this particular recording works better played back S/A (note: I had to re-edit this, as I meant sherzo/andante, and not andante/scherzo). For one thing, Abbado's andante is relatively swift - less than 14 minutes - so it provides a shorter bridge between the first two movements and the finale (when played S/A, that is). Second, Abbado's scherzo is nice and swift (I prefer it this way) - a tempo that's nearly identical to the end of the first movement. Therefore, it fits perfectly when they're butted together - the scherzo feels like a continuation.
Here's my skinny on this: if you're going to turn Mahler's andante (moderate andante!) into a full blown, Bruckner-like adagio, then put it right after the first movement, when your listeners aren't feeling fatigued yet. If you're going to do the scherzo at some tempo that bears little or no resemblance to either the end of the first movement, or the very beginning of the symphony, then place it third so that the listener isn't asking this question: why is this movement even here?!? MTT/SFSO is prime example of this very problem, so I find that it works much better played back A/S. I feel the same way about the Karajan M6 too.
Interestingly, Michael Gielen chose to do his scherzo (placed second) at the very same slow tempo as the beginning of the symphony. It's different but it works (and it helps that he doesn't drag the numerous trio sections). He follows his slower-than-normal first two movements with an andante that's closer to 14 minutes, and a finale that's at the standard 30 minute length (I don't care for 33 minutes, except for Tennstedt II).