A few days ago while I was still in the Bay Area, I visited the new Academy of Sciences museum with my family. They just re-opened a few months ago after replacing their old earthquake-damaged buildings with a new, very unique building. You can follow those links to learn all about the 'living roof' and the various exhibits.
I have some mixed feelings about the new museum. The old museum (you can see some pictures of it at their time line page) was a funky amalgamation of several buildings built over many decades. You could see the history of modern American natural museums in one place. The old section had dioramas of stuffed animals in pseudo-natural scenes. Exhibits like lions hunting antelopes with Serengeti sounds playing on speakers. The newer sections had live animals and fish and a greater focus on education. The whole place was labyrinthine and dusty, and a well-used kind of ancient. It was never too full of people. I liked the old museum and I'm sad that a piece of my childhood is gone.
The new place is very shiny, flashy and popular. We waited for one hour and forty minutes to get inside. It might be bigger in cubic meters due to the higher ceilings, but I don't think it's bigger in square meters of floorspace. The main exhibition areas are limited to the two ends of the building, past the planetarium and tropical sphere, and the aquarium has been moved to the basement. The aquarium is quite a bit nicer than it was, with a few tanks that rival the Monterey Bay Aquarium in quality and cool curving Plexiglas, but not in size. Like the Monterey Bay Aquarium, the museum pushes education on choices the individual can make to positively change their effect on the ecosphere. They have a 'carbon balance', but it mostly ends up being played with by children who generally don't decide whether to buy a SUV or a hybrid car.
I found a couple things I really liked; click on the thumbnails above. Read the tag on the human skull, and take a look at a whole wall of very carefully pinned ladybugs. I took three pictures a various zooms. That may have been a PhD thesis, right there.