As the title says, the commands from File->Scripts should be moved to File->Export/Import/Automate, don't make new users have to know that for example Image Processor is a script, it's an automation function and as such should be in File->Automate. Analogy: you shouldn't have to know how a car works to be able to drive it.
Load files into Stack should go to File->Import and be changed to something more meaningful, something like File->Import->Files into Layers and the same with Load Multiple DICOM files and Statistics. Layer Comps to Files and Export Layers to Files should go to File->Export and the remaining scripts should go to File->Automate. All that File->Scripts should hold are Script Events Manager, Browse and the user created scripts.
And on a different (but still related to usability) note, what's up with Flip and Flop in the Vanishing Point filter?