I think it would be very useful if in the list of annotations which is below the sequence view, there were check boxes beside each annotation, and beside entire groups of annotations, which you could check and uncheck to show/hide that specific annotation. I know this can already be done in the annotation highlighting popup menu, but I think this set up would very much streamline the process. Thank you for your considerations!

I agree that that would be useful. Correct me if I'm wrong, but I believe He wants to be able to hide an specific annotation and not a complete set of the same kind (so, option 1). Currently it is possible to hide all of the same type, but not just one of them. That is useful, for example, if you have a lot of annotations in a plasmid but you want to hide most of them and just show the most important in a presentation. So far, I've been just creating copies and deleting the ones I don't want to show...