If you have a change to visit the Tokyo Science Museum, it's quite good in this respect - it has a lot of interactive displays, many of which are very hands on, and some are application based - focused on how the science concepts are used in industry (with some occasional corporate tie-ins, which weren't too over the top). It's fairly kid focused, as others have mentioned - most of your competition for seeing the exhibits will be school student groups.

Incidentally, the building is featured near the end of the Shin Godzilla movie.

Are you talking about the one in Kitanomaru park, or the Miraikan, on Daiba?

The 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).