Well, a few things.
First, there do remain a few applications that are not currently supported by the capture key. (But wait, if you write a custom capture script, will it run/work if you invoke Capture With Options? If so, are the |tags|, |sourceURL|, etc. applied before or after the Capture With Options dialog? I haven’t tried yet.)
Second, If you capture text or an image from within a document via the EagleFiler:Import service menu item, then there is (currently) no way to tag, annotate, etc. during the import (the same situation that existed with F1 capture before this new feature).
And finally, I have a script that imports emails as text (yes, I know, but I have my reasons). The script asks for the library and tags during import, but it would be nice to also get notes, label, a title, etc. without having to throw up a dozen dialogs.