An alternative solution for when saving a site as a template doesn't work, whether it's for size reasons or other reasons is to use the Office 365 PnP poweshell.  

https://github.com/OfficeDev/PnP-PowerShell

Using the Provisioning Engine built into the powershell, you can quickly extract a template of a site using Get-SPOProvisioningTemplate.

While this doesn't completely replace the export site as template.  It's the best solution I was able to use for this situation recently.