One of our customers had a SharePoint 2013 based intranet portal which was a mix of SharePoint OOB features like content types, search, workflows, InfoPath as well as many custom-built SharePoint web parts that were talking to custom SQL databases. With 150+ sites and thousands of documents being accessed by users every day, it was really challenging to migrate the content w/o any data loss as well as downtime. Another biggest challenge was to migrate custom applications that were built as a conventional server-side web parts to the latest SPFX solution! The planning and design phase was key to this migration which actually results in a smooth migration over to SharePoint Online.
