In a minute, I will show you how to change the site collection administrators for all site collections using PowerShell. Thanks to Maarten Peeters for helping!
If you are using MySites and personal sites have been created, you might want to use the following, to exclude the MySite site collections. Please check if you are using the "personal" managed path. If you are using a different managed path, you can change the "*/personal/*" to reflect your environment.
I hope this helps someone out there to save some valuable time!