I'm curious what features you plan to do next. Have you posted about that somewhere? Here are a four possible minor changes that could save the user time. What do you think?
1. Select Content sometimes makes small selections on blank pages. To remove them we now have to click one thumbnail at a time, wait for the image with selection to appear, right click the selection and click "remove content box".
Quicker solution: having a "remove content box" command in the right click menu for the right pane (thumbnails). Users can then select all thumbnails with this problem in the right pane (doing a height sort tends to group them) and click "remove content box" once and for all.
2. After running Select Content on all images there can be need to edit the selection manually (decrease/increase height or width) for some images.
When clicking a thumbnail ST reruns Select Content for that image. That takes 1 to 2 seconds extra per image.
Quicker solution: having a special key (for example: Alt) that prevents reprocessing when held while clicking a thumbnail and instead displays the selection from the first run.
3. let users customize default margin size, maybe through an ini file.
4. let user customize (add) values to the dpi suggestion list (300x300, 600x600 ...), maybe through an ini file.