[ivyart]

Well... that is a tall order.
I suppose the museum in Ueno is not so bad. The Mori Museum seems well... is more interested in splash and flash than Art and Ideas. Many of their shows begin on excellent premises but end up going beyond curatorial control, or the perimeters of the exhibitions collapse under the inability to collect enough specimens to fluff out the shows.
Most smaller museums/public art spaces tend to be run by civil servants who have no art background- get a Government job and they just place you somewhere, anywhere and Violla you are workin' in the art world now. So unfortunately the galleries control the museum staff and programming, and through "honest" ignorance are sincere, but unwilling shills for a few less than scrupulous galleries.

P.S. if you don't believe this, look closely at where the museum artists are represented, then try finding an (living) artist in a museum who does not have a financial allegiance to a local gallery. This might be less apparent had tokyo more than ~25 semi-serious galleries.