The discontinuity involved in the collapse of the wave function is a total hack. And there are a whole lot of magic numbers (pi, the speed of light, etc.).

If there's no possibility of an undo, I'd at least like to see a pause button.

Re-enable cold-fusion. Rather than fixing the bug, they should have just documented it and made it a feature.

The class hierarchy should be re-designed. As it stands, it is often impossible to tell exactly which class a given object is in.