Probably the most confusing part of LoadImages is the metadata extraction and more complicated matching of file names. Perhaps instead of just giving a regular expression matcher, allow people to build the expression. I'm envisioning a list of items that can be added: "Exact Text" "Repeated Character" "Metadata Field", which the program can use to build the appropriate regular expression.
For a first-time user, the pipeline concept may also be a source of confusion here, but I'm not sure what much can be done about that except maybe for the first time someone runs the program, presenting some links to introductory documents might be useful.
As for IdentifyPrimaryObjects, one thing is that some of its action is hidden. For instance, cropping a previous image based on another IdentifyPrimaryObjects module will allow you to use "Per Object" thresholding, and there's no error indicator if you try to use Per Object on an image that hadn't been previously cropped. This is a source of confusion because a novice user would assume that any object-finding based on a previous object would be considered a function of IdentifySecondaryObjects and not IdentifyPrimaryObjects. The biggest way this could be solved, perhaps, is to extend IdentifySecondaryObjects with this ability and strip per-object methods from IdentifyPrimaryObjects. Though I recognize this could break some previous pipelines, I don't suppose it would be too hard to include code to check whether the loading pipeline has an IdentifyPrimaryObjects module using a Per Object method and then, with a notice to the user, automatically converting it to an IdentifySecondaryObjects module.
The other big problem here is that, as Marc mentioned, that testing different options can be a pain. With so many different methods and options to choose, it would be a big usability improvement if it was possible to see the results of an operation dynamically. Test mode can help to some extent, but it is hard to see how the objects change, especially since it is not translucently overlaid onto the input image. It would also help to be able to flip between the loaded images, not just the one . And then if you want to test it against multiple image sets... It's all really oriented to people who think like programmers, and not necessarily people who just want to do something.
Since we're talking about usability here, I'll also throw one other pitch in: a Module that acts as a divider to visually separate different parts of the pipeline from each other (which could perhaps also call ConserveMemory). I don't know about others, but I'd like to have a visual way to separate operations on one loaded image from the next, or background correction steps from object-finding steps. And/or put the name of the output item next to the Module name in the Pipeline list, so that users can easily see which module does what if they have multiple modules of the same time.