Add your FULL Side by Side right aspect ratio to 16:9 adding the following TAG into your YT's 3D videos:
yt3d:aspect=15.99:9

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NO TAG | SbS and Anaglyph

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WITH TAG yt3d:aspect=15.99:9


WITHOUT TAG yt3d:aspect=15.99:9

So adding the 15.99 tag lets us upload full 1080p side by side, which Youtube viewer then outputs in the selected 3D format? That sounds nice! Never liked the resolution loss of original --> cut in half to SxS --> recompression on Youtube. This could produce some very nice 3D!

May be I will go test a short clip!
Ed