[Sparktank]

It's common to see 3D blurays to have variable black bars on the sides to increase 3d parallax.
Usually the black bar is on the left, and can skew angle.
On the actual 2D disc (not 3D with the left-eye/avc), there won't be missing image data.

Some 3D movies are opened up to open matte (1.78:1 on BD).
Jumper (2008) is originally 2.35 : 1, but the post-production conversion to have it on 3D-BD, it was changed to 1.78:1.
That would defy the director's intended aspect ratio, if you swing that way.

Some movies oversaturate the colors and really tweak the brightness levels.
The brightness issue was observed greatly in the third Transformers movie: Dark of the Moon. The 3D-BD for Transformers: Dark of the Moon came in too dark for most home consumers.
Michael Bay supervised the 3D-BD transfer and said it was accurately transferred to disc.
According to Bay, most home consumer TV's weren't created to display such accuracy, thus giving wrong perception of brightness.
Which probably led studios to oversaturating and brightening movies like Guardians of the Galaxy.

It's really different for every movie.
You'd have to sit through both viewings to actually see if there is a difference in quality.
If you have to change your display or playback device once, then that's the not the version of the movie for you.