Glad you liked it.
I think the scripts plugins (java) are better suited to modify the Batch XML which opens the door for easy implementation of database lookups, web service calls, validate/in-validate fields, changeing the document or page order and even improve classification results. Even though they are compiled at run time, It might be better to use a custom plugin to manipulate the images or other cpu/memory intensive plugins.
Did you know that we have a guide on how to create plugins for Ephesoft here: http://www.ephesoft.com/wiki/index.php?title=Developers_Guide
You can use Imagemagick calls to perform all these image enhancement methods you mentioned.
By the way, The enterprise edition includes Recostar engine. Recostar comes with deskew, despeckle, auto rotation, line removal, shade removal, punch whole removal, converting white-on-black test to black-on-white and many more out of the box. Oh yes, Recostar can save the result image if you want to so with Enterprise, we already have these features.