Don't have 3D glasses either, but the video has framerate issues. It's very choppy.
The 3DS screen runs at 60 fps, but considering a 3D game has to render each frame twice, I guess it's safe to say that most 3DS games run at 30 fps.
Now YouTube only accepts 29.97 fps anyway, so I should have worked out just fine. But it didn't for some reason.
Basically, what I would have expected is a video with frames like:
1 2 3 4 5 6 7 8 9... (i.e. all frames are unique), but instead your video is
1
2 2 3
4 4 5
6 6... (i.e. every other frame gets duplicated)
So in the time a regular 29.97 fps video displays 9 frames, your video can only display 6 frames. The framerate gets cut short by 33%, which means
that your effective framerate is... 19.98 fps, which is lower than what you see in cinemas (and cinema movies typically have motion blur, which makes the low framerate hard to notice).
I suggest that you drop the raw .avi into VirtualDub. Move to a time where there is some movement, like while playing a Mario stage. Now use the arrow keys to advance frame-by-frame.
If you can still see the duplicated frames, then the problem already happens while capturing. If there are no duplicated frames and the video looks smooth, then YouTube butchered it.
Good luck trying to fix that. Wouldn't want to watch a 19.98 fps video

...
Edit: Haven't examined the real 3D video yet, but at the first glance it looks like it has the same problem.