Admittedly, this is also somewhat played with in terms of authenticity as the DunBroch tartan literally can't be made in the traditional methods.
Executive Meddling: The original director Brenda Chapman was replaced for having ideas that the suits didn't agree with, which many have assumed had something to do with the film's feminist message. She notably thought the final product was faithful to her vision.
It is not that unusual for a Pixar film to change directors half way though: the same happened with: Toy Story 2, Cars 2 and Ratatouille
What Could Have Been: Much of the film was originally to be set during the winter, with snow being the big technical challenge for the film. But when Brenda Chapman left the project, so did the weather.
The first summary released online stated the three Lords actually aided Merida in breaking the spell! That did not happen, to say the least.
Another summary implied that the three Lords were direct antagonists to Merida.
Mor'du's backstory was supposed to be more prominent in the earlier draft, thereby making the film much darker than it already is. Inevitably, executives made Pixar tone it down.
The movie's official artbook confirms that originally, Young MacGuffin is the one Merida ends up with. This was probably cut out of the final product since the filmmakers wanted to focus more on the mother/daughter relationship.
The film in general gets this; as revealed in a number of the home release featurettes, although every film Pixar (and any studio for that matter) makes always has sequences that get dropped, Brave specifically has an immense amount of scrapped and altered scenes that just didn't make the final cut, made harsher in that a lot of the sequences were nearly finished.
The directors commentary reveals numerous scenes and ways the film could have gone but they decided not to do for various reasons. The main change was that there originally would have had snow for two thirds of the film. They changed this due to the fact they felt it would ruin the Scottish Landscape.