Default mirrors may not be the best ones in terms of download speed. Allow users to manually pick a mirror for binary download.
Timeouts in one file cause the whole metadata download process to be re-started. It would be beneficial, if the user could resume/retry the current download after a failure.
Currently, the user can uncheck unnecessary Temporary Repositories to avoid downloading all metadata. However, each repository must be unchecked one-by-one. Select/de-select all button would make it more efficient for the user to manage the repos.
Remember the which Repositories the user has deselected earlier, and ignore them for future sessions.
Let the user choose broad "groups" that they are interested in, and remember this choice. For example, there is no point getting metadata for Android/UWP packages or showing these packages in the "Selection Tree" if I'm only interested in Desktop development.