Site validation has been tightened. Previously, only the language code and project name had to be valid - now, they must be a valid combination (i.e. en.wikiversity exists, and so is valid, but sco.wikiversity is not valid, because no such wiki exists).
When the global watchlist feed is loading, an OOUI widget will be shown, rather than an animated gif.
An option has been added to no longer group edits to the same page. For now, this isn't very useful, since metadata for the edits (editor, summary, tags, etc.) are not yet shown, but they will be soon. Until then, ungrouped edits are treated the same as pages with only 1 edit - the minor and bot flags are displayed if applicable. If edits are grouped, the minor and bot flags are only shown if they apply to all of the edits.
Starting with version 5.0, there will be an option at the settings page to switch to and from a "stable" version of the script. When activated, the script import in your global.js should be replaced, and then the page refreshed with the new script loaded. The stable script will live at User:DannyS712/Global watchlist/stable.js, and will be updated with each full release. Otherwise, it shouldn't be edited, providing a version that is less prone to bugs as the script is developed.
WARNING: Starting with version 5.1, the option to mark the pages of a site as seen be implemented using the entirewatchlist API option, rather than manually listing the titles. This is being done to simplify the implementation code. This will result in the same functionality as marking all pages as seen via Special:Watchlist (i.e. even if the page isn't visible due to your filter choices, it will still be marked as seen). If you would like to keep using the current method for a while, please switch to the stable branch.
Version 5.0 has just gone live. It includes the new features mentioned above.