I get the articles point. I too feel as though things should be more actual hands on, less flash-game-y.
But one kinda-counterpoint was my experience in Amsterdam at Micropia [0]. Museum containing many small things including fungi, bacteria, ants etc etc.
Some stuff you didn't want to actually touch with hands really anyway...
Yes they had magnifying glasses but many exhibits were simply using the screen to show the image from a microscope. And they let you control the microscope to focus, zoom in and out, etc.
Left an impression on me as being a museum that did digital right.