Just want to add a few notes to this thread for posterity, since I've encountered several people now who have noticed this problem:
After messing around with several more systems (upwards of 30 now), my working theory is that there are
two different panel types being utilized for the upper auto-stereoscopic screen.
Type A is the most common and
all that I've seen suffer from the interlacing problem.
Type B is a bit rare but does not suffer the interlacing problem.
However, it has a much narrower viewing angle (noticeable washout occurs at 20 degrees vs 40 degrees on type A), slightly higher black levels which makes the picture appear a bit undersaturated, the parallax barrier adjustments (ie super "stable" 3D) occur with a noticeable judder rather than type A which is fairly smooth, and finally ghosting/crosstalk is a bit more noticeable than on type A.
It is unfortunate to say that this is thus a panel lottery with no distinguishable features to tell without opening the box and finding out (assuming you can see any of it), as the serial number is the only marking and the panel distribution seems more or less random, with both older and newer production batches having both types.
That said, like panels seem to occur together -- I have a QW1021 black and QW1022 red that are both type B. There was also a QW4014 red that had type B, but it was oddly FW9.4. I've been unable to locate anything remotely close to 4014 in series.
For what it's worth, type A actually seems like the
overall better panel assuming you can deal with the interlacing, especially considering the stabilized 3D encourages off-angle viewing. I would only recommend type B overall if you mostly viewed the 3DS head-on to begin with, and wanted a N3DS for the other upgrades.
I've finally settled with one of my units and wish anyone else having this problem good luck
Edit:
Upon closer analysis of the viewing angles of both types, I realized a striking difference in that type B not only washes out but gets brighter the wider the viewing angle gets, until the entire screen is nearly a bright white at 90 degrees. Type A merely washes out and actually seems to get dimmer at off-angle viewing.
These are definitely two panels that were manufactured to slightly different specifications.