Multilayered work of art. It could be read under several perspectives. Undoubtably, one of them would identify the witch with the Catholic Church, in a ivory tower, self indulging in a sort of chapel decorated with beautiful images of saints (that may risk to hurt some sensibilities). I would not be surprised to hear Gilliam saying that. However, honestly, I don't think the film is anti-catholic. It looks to me like he meant to show a contrast between rationality (the French general would represent all the lucid and merciless values of the Enlightenment) and its opposite, proving that ratio is not enough to deal with the inner realities of human beings. Then this would be equivalent to criticise the Church, and probably any religious movement, when they fail to fullfill their proper mission of giving meaning to this gap. I may be overinterpreting, though.
Another possibility, which may be superimposed to the previous, is that he tries to show how women deal with evil. The unavoidable comparison is with Lord of the Rings, in which the evil deal with the reality of the world mainly through men.
Certainly the film is about abuses,
metamorphosis (after all growing up is a big change), finding the right direction in a changing environment.
It's dark, I don't think this is a film for children. It is rich in Christian iconography.
Millais Ophelia is used as the base for an entire scene.
Some note on style: Gilliam decided to give a lot of freedom to the actors. I don't know whether this is only an experiment or a line that he intends to follow in his future work. At the moment the technique is not refined and sometimes scenes look like episodes, stopping the plot for some while. But it's only my opinion...
