How to delete my itunesconnect app with status "Prepare for Submission"?

You can change it here (follow the red square as shown below)

In my case i accidentally entered version number '6.0.1' when i actually wanted '6.1'. The 'version' field is editable. when you change it and hit the 'save' button (give it a second..) it will change.

There is no way to delete an app in that state, according to the iTunes Connect Developer Guide.

Apps that have not been approved yet can’t be deleted

The only thing we can do for now is to change the name and bundle ID until Apple changes its mind.

Edit: Seems that Apple finally made this possible according to Leszek Szary's answer here