I thought that the fur 'bug' got fixed?
With the professions, I think that the professions should stay how they are, but at the Academy, you can choose a branch-off job for your profession, like weapon-smith, tank, spy, doctor, librarian, etc.
Also, do you mean the storyline with the crates? I think that adding it back would be okay as it would allow you to know where Irving is for the upgrading of the weapon, but what REALLY needs to be put back is the fight in Bootleg Pass. Taking that out damages the Bible-oriented part of the game. Irving and the boxes, not so much.
Caleb's map: indifferent ;0)