There is no mystery as to what went wrong with this production, Mark left becuase his vision was against that of every other person working on the film (to quote Baker he just "didn't get it"), having to replace a director that late in pre-production was a problem, no 'visionary' director would come on board becuase it was too late for them to make any significant changes to make it their own film.
Joe Johnston was hired, they made the movie, Produces felt the werewolf scenes were too tame and wanted to pump them up a bit, as well as change the third act to match Walker's pre-Johnston script (werewolf vs. werewolf) thus there were six weeks of re-shoots.
Because of this delay Elfman was no longer able to score the film, he had other things he had to do. So new people were brought in.
The film is now being re-edited by two of the most talented people in the business indicated that despite the troubled production Universal has faith that the film has the potential to be great (if not they wouldn't be continually pouring money into it and going out of their way to re-edit the whole thing despite generally positive screening reviews)
This is not a case of the studio not understanding the movie - unless wanting a fiercer werewolf and bigger climax counts as not understanding the film... which I guess is possible but from the amount of money and talent they continue to pour into this production I just don't think its a case of studio heads "not getting it".. I mean the producers sided with Baker on the were-wolf design and went back to the Walker scripts climax rather than going with the one rewritten by whoever Joe J brought in.
OF course they then made the decision on a fully CG transformation but based on the footage I've seen of it (trailer) it looks great so doesn't bother me at all. I can see why it upset Baker though.
FIN