Big changes needed for onedrive for business
1) improve the feedback of what onedrive is currently doing. At the moment you can see its processing files but what file or folder? I have thousands and it keeps counting up to 8000 and then starts over again, no errors no problem reported just doesn't tell you whats going on.
2) I think the whole syncing sharepoint document libraries to onedrive for business is a huge joke right now. This whole situation has wreaked me in front of a client which needs to access files online but it wont upload.
If you have a large number of files, try mapping a network drive to your SharePoint Online document libraries instead with a tool like Zee Drive http://www.thinkscape.com/Map-Network-Drives-To-Office-365-OneDrive/. Zee Drive can work with very large document libraries