I upgraded to WordPress 2.0.1, which ended up taking shorter than the last time. This time there were however more individual files and directories to delete: I feel tempted to write a shell script to do this for me next time. It’s pretty annoying to go into a specific directory and delete a subdirectory. Or a specific file.
If you have shell access, this is a good way to become millionaire! Install and upgrade WordPress!
And oh: WordPress plug-in structure actually sucks. They should look into the way how the NucleusCMS guys do this.