Went today with the girls and have to say I was a bit disappointed. Cost us £42 to get in - me, dh and the four girls which was a bit of a shock. Got 'escorted' around the place and were out within 2 hours. Thought there would be more interactive activities for the children. Was a shame we couldn't have spent more time there. Also, personally as a believer in creation, was rather annoyed that half the exhibitions talked about evolution as a fact rather than a theory. That being said, the girls did enjoy aspects of it - the rainforest and the dome in particular.
However, as we found we had plenty of time left we went onto the National Museum and the girls absolutely LOVED it! dh was also very impressed as it was free
So for a good day out in Edinburgh I would say, save your pennies and visit the museum.