Jon Favreau (who not only directed Iron Man, but also one of the best family films of the last ten years, Zathura) has said on numerous occasions that despite the similar basic premise (someplace where things come to life at night) the film will be nothing like Night at the Museum. The tone will be darker, less focused on slapstick humor, more focused on adventure and old fashioned "Disney" fun.
I think this movie will do really well if they market it properly. Market it like taking a mini-vacation to Disneyland, except all you have to do is drive to the cinema.