Without doubt the remote files-per-folder.
For OneDrive, the max files per folder is still 5000. Using the default DBLOCK size of 50 MB, the maximum amount of data per backup is about 125 GB (2500 DBLOCK and 2500 DINDEX files, 2500 * 50 MB = 125 GB). The number of backup versions reduces this (one DLIST file for every version). The amount of modified data in the available backup versions reduces it further. Uncompacted DBLOCK files could reduce the maximum backup data even further.
So with OneDrive’s 5000 files limit, I guess the maximum protected source data will be somewhere around 80 GB, which is way too small.
This limit forced me to increase the DBLOCK size to 2 GB for my backup job that protects 4 TB of videos and uses OneDrive as storage provider.
3000 subfolders with 3000 files per folder would increase the 125 GB limit to 200 TB, which is virtually unlimited.
For larger backups, I agree that you should choose a larger DBLOCK size. Even more important is to think about the internal block size (in my videos backup job, I increased the default 100 KB th 10 MB). Increasing the block size will drastically reduce the local database size (database of my 4 TB backup is about 80 MB, takes about 10 minutes to recreate!).