I have a few observations from my personal experiences and what I've found to like and not like.
Firstly with display cases, I have found display cases which are mounted flush against the walls of the room to be quite aggravating. As an enthusiast I do not want to be limited to seeing only one side or view of a piece. Light is extremely important not only for viewing but for taking photos. To few museums take into account that many visitors will want to take photos. The only way to allow for this is to have as much natural light as possible in the display area. My suggestion for display is to place the cases in the middle of the hall, making the pieces viewable from all sides, mount pieces where applicable on clear plastic mounts without solid backgrounds (what I mean is to avoid the type of display were the sword is mounted on say a red fabric background). From the couple of pictures you posted it appears that your building already has windows in some of the halls? This is wonderful I think, to often arms&armor displays are dimly lit. In general I like galleries that feel open and airy and allow me to decide my viewing angle. Having a selection of couches or benches in the gallery is also always appreciated.
With regards to materials to be displayed I would put a heavy focus on creating displays with mannequins, costumes, and props when possible, I like seeing a "scene". Perhaps a large display along these lines could be the centerpiece of each gallery with additional cases displaying accompanying artifacts. Personally I think it helps bring pieces to life to see them in context and helps generate interest from the general public who would otherwise find them somewhat boring. For exceptional pieces however, I personally appreciate "stand alone" displays for maximum viewing where the piece is not at a viewing disadvantage from being in context (such as belted at the side of a mannequin). Decorating the galleries themselves to go with the theme of the objects on display might also be a consideration. I like the feeling of changing time periods and places when I move from one room to the next, rather than having the same old "museum room" feel to every gallery.
In terms of written material to be displayed with the pieces one thing I wish museums would do is give more detailed descriptions. To often a piece is only accompanied by a small card giving the dating of the piece, country or tribe of origin and little else. Using period illustrations and photographs to accompany the description would also be very nice to see.
I'm looking forward to seeing this thread develop, I think some very useful and insightful ideas will come out of it.
I'm actually planning to be in Krakow this fall so I'm rather excited hear about the items on display and what direction the displays might go. I'm certainly planning on making a visit, from the photos the museum already looks quite nice.