I would do it the same way...parent profile for the 3D version with child profile for the 2D version.  This is also how I am seeing it done for the very few 3D/2D/DVD sets I own.

What the Martian said...that's how I do it. I then lock parts of the 3D because I delete the BD and/or DVD references from it including the disc info list so DVDP will go to whichever one I insert in the disc drive.

Box sets contain more than one film. Different versions of the same film does not qualify imho.

While the rules do not mention this type of set, they do define a Box Set and this does not, in any way, shape or form, qualify as a box set.

Quoting mreeder50:

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Quoting Parsec:

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...basically because the only difference between the 2 is the "3D", the audio and everything else is much the same on both discs...

Not true, there are different extras on each disc. If you are looking for something specific and don't have separate profiles you'll have to put each disc in to find it. At that point the child becomes very helpful.

Actually you'll find that the 3D disc usually has no features at all. They add them to the 2D disc because of the space available (also it then becomes the same disc they use for just normal BD 2D releases). Sometimes they even add a bonus features disc. 3D takes a lot of space, look at movies like The Hobbit and the recent Titanic 3D release - those 3D versions are in fact 2 discs in themselves, they don't have room to add features, they are on a separate disc.

In this case, all the features can be added to the profile using the same rules as used when adding features from a bonus disc.

What Rizor said.

So then if you guys believe that. Then what do you do when you buy a 2 disc edition of a movie on DVD where one disc is basically 'bonus features'? The way you are talking, you want to profile the bonus features disc as well.
The features on The Life of Pi 3D disc are in 2D. This would make things even more messy as with a child profile for the 2D you'd sort of think the features listed on the 3D are in 3D and the ones on the 2D, in 2D.

The whole thing is messy, the rules really need changing, so do a lot of the options in DVDP.

The contribute process is not as selective as I would like, that doesn't mean you can't contribute what is with in the rules by marking the appropriate boxes.

Just because I like to profile a bonus disc that has info I would like to be aware of, doesn't mean I would contribute it.