If the list view threshold is preventing you from getting all the items in browser view then there is no way round this (other than upping the threshold limit, though not an option in SP Online).
If you install the SharePoint Online Client Side Components you can use these in Powershell with CSOM and CAML to either:
a) issue a CAML query to get all items where Content Type is not equal to 'Folder'
b) issue a CAML query to get all items, then check each one in code to see whether it is a folder
I will post the code for this shortly as I was trying to write it but have hit a problem myself trying to get the ContentType field.