Time Machine ridiculously slow after El Capitan upgrade
Part of the issue is that low priority input/output-operations (I/O) now seems to get throttled heavily. You can check it via Terminal (can be found via Spotlight (usually bound to ⌘Space) and entering terminal) then entering at the bash prompt:

fs_usage backupd


and look for the THROTTLED entries. If you see them, the backup is throttled.

So if you have a ton of files, just the time it takes to do the I/O takes forever, even if the files are small (because it performs a bunch more I/O operations around xattrs etc. than it used to).

Go to a Terminal and enter:

sudo sysctl debug.lowpri_throttle_enabled=0


For me, this speed it up from 72 hours to ~4 hours on an filesystem with 2.5 million files.

It's also a good idea to re-enable the throttling after your backup finished successfully with the following command

sudo sysctl debug.lowpri_throttle_enabled=1