Are you talking about the one in Kitanomaru park, or the Miraikan, on Daiba?
replyThe Miraikan, in particular, is a fantastic science museum. I think it suffers a bit from what the OP is describing -- and also, a lack of English -- but for the most part it's interactive and uses technology in a really innovative way that goes beyond iPad fluff (an interactive seismograph room comes to mind, where you could move around and see the systems detect your movements in real time).
Ah, the first one is where I went - 科学技術館 (Kagakukijutsukan) in Kitanomaru park between the imperial palace and budoukan. It has some english (but, as always in Japan, knowing a little Japanese greatly helps), and the exhibits are fairly self-explanatory.
replyGood to know that there's another nice place to go.