That's because it does file-by-file which means the computer has to open a connection, download the file, and close the connection so you are losing most of your internet speed because of this.
It doesn't matter if you're on Dialup or 100MB/sec, a 5 kilobyte file is still downloaded in a split second, and the connection open/connection close still take about the same amount of time.
The best way that SE could fix this is update the Seekers Edition Download so that the files contained within aren't 5+ years old, so the user doesn't need to download 5 years worth of game updates and anybody looking to return could download the newest Seekers Edition from the website and it would actually be faster to just reinstall altogether.
That, and now that we have ONLY the PC version.. another thing they could do is looking into releasing .zip files that contain all of the changed files that users could download, and it would dump the files directly into a POL folder, run POL then POL just needs to take those files and put them where they belong for an update that only takes 30-90 seconds.