I remember the old one too... didn't care for the new one. Miss the snakes and lizards. New aquarium feature is better than old one, but pales in comparison to Monterey. Rain forest display is pretty dull after a long wait in line to see it.
The new Academy of Science is very good, been when I was a kid, and now as an adult it is still a very interesting place to visit. I don't like the big crowd also, so I would suggest to go there during the weekday(school hours) and not a first Wednesday of the month. Check out their website, somewhere will have a schedule for free admission if you are SF resident.
It's pretty bad ass the way they've redone it, but I have some pretty fond memories of the old crusty building. Some of the props from the old buildling have been placed in random locations around the new one and they look out of place to me. In high school we used to load up the bong in the parking lot and watch the late night pink floyd laser shows in the planetarium. I've been to the new place twice and didn't get a chance to go in the new planetarium because of the extra cost and the lines. Again, it's cool, but not the same as it was.
I had always thought Academy of Sciences was pretty neat as a kid. However, I went recently and was disappointed with how quickly I was able to go through the whole place. It will keep you interested for a couple of hours but don't plan on spending half the day there.
Its MODERN, so in that aspect its cool. The part where all the stuffed animals are kept, was a let down. It seems like my old aunts place with the taxied animals starting to frey and rot. I really enjoyed the rain forest exibit. Lots of little things to look at.