[Berkley]

Michal,
As a preliminary inquiry: Will you be working within the limitations of an existing buiding, or starting from the ground up with an architect? If you will be using an existing structure, what flexibility will you have with regard to the size and shape of exhibition spaces, natural lighting, and the flow of visitors through the exhibition space. Unless you are just asking for idealized "if I were King" fantasies, these mundane considerations will have a considerable impact on the design that is best for your collection and its intended audience, whose nature and size will also be important.
What a wonderful opportunity you have! This should be a very interesting thread to follow.
Berkley