The question begins with an incorrect assumption. Currently, when movies are made, they are mainly made for 2D setups (i.e. theaters, and home systems). Due to the different ways films are made, this has to be broken out into different options:
- For live action films where they are recorded in 3D, they can just use one of the two images they've filmed for the 2D version. There shouldn't be a 'bad version' as the question supposes, because if there is a marked difference in quality between the two, then that will negatively impact the 3D presentation of the film.
- For live action films not recorded in 3D, they have to alter the 2D footage to create the 3D footage. This is called post-production conversion.
- For CG animated films, they'll create both in concert, and will sometimes create subtle differences created in the 3D version. (see Tangled for example)
- I don't know of any non-CG animated films that have been released in 3D, so I guess this is one is unknown.
Comparison shots of Tangled's 3D and 2D versions follow. You can see the differences in the backgrounds, look at the trees and see how they're in clear and in focus in the 3D version, but blurry in the 2D version. Similarly the fields in the background are clear in 3D, but blurry in 2D.