This should be fairly straight forward. There are two problems. Selecting which columns should be displayed in the UI is buried deep within the preferences under something called "Entry table columns" but you need to know the names columns to display. The first thing is to change the name of the Entry table to something that a normal person would understand like "Main Window" or even better, just lump it all under something called "Display" which avoids the need to name something which is difficult to name.
What I would do is get rid of the "Entry Table" and the "Entry Table Columns" and lump it into "Display". Split "Display" into two sections: Citations and Application.
The second problem is that a user has to know the names of the columns to be displayed. That should all be checkboxes with default column locations and widths. The column widths are meaningless to people. If anything, they should update automatically upon clicking the window but get rid of the whole thing. Replace the "Entry table columns" with "Columns Displayed" as a set of checkboxes with the names of each column and perhaps a brief description. Don't worry about ordering the columns. Users will intuitively do that through the UI. Also don't worry about placing added columns in the right place for users. If a new column is inserted in the default location, the user will move it. If that column is removed, the location that column was in needs to be saved. If added, the column should appear where the column last was.
BTW, I do UI and usability work professionally. If you want or need tips and advice don't hesitate to ping me.
Related to:
https://sourceforge.net/p/jabref/feature-requests/299/
https://sourceforge.net/p/jabref/feature-requests/714/
https://sourceforge.net/p/jabref/feature-requests/412/
Last edit: fdar 2015-08-05
@Ben, we need your help :) Are you still available? Could you get in touch with us at https://github.com/JabRef/jabref/issues/104?