Here are two very iconic issues with bookmarks that I'm sure many would agree upon tackling them.
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The ability to choose the order of the bookmark that gets added in a folder. Right now, every bookmark we create, is added on top of corresponding list/folder. It would be ideal to give an option to select the opposite behavior, so that the new bookmarks go to the end of the list, if chosen so. The same is true when you move single/multiple bookmark(s) between folders in bookmark manager. Why not have the option so that they could be added to the end of the list instead of top?
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The ability to drag the bookmark and change the belonging folder without having the folder view or bookmark context being closed upon dropping in new location (folder/sub-folder). The disappearance makes you repeat the procedure again if multiple relocations are needed. I know, someone would argue that bookmark manager makes it easier; Still, this is not an acceptable excuse to justify the disappearance.