Hi Burr, it's because of the history data that's attached to every output point. Part of the history data is a list of all inputs that were sent into the command that created that object, and in this case you have 2500 inputs so there's a pretty substantial chunk of text data attached to every generated point there.

This is one of the reasons why I want to restructure the way that history is saved more in a central list of actions rather than as data attached to output objects.

If you remove the history data you should see the performance issues go away, you can remove history data from the selected objects by using this script here:
script: /* Remove history data from selected objects */ moi.geometryDatabase.getSelectedObjects().callMethod( 'deleteHistoryData' );

The delay that you see when deleting things is when the undo mechanism is gathering and compressing some big chunk of history data to save to the undo list.

Once you remove the history data both deleting and file saving should work more as you would expect.

- Michael