I recently updated to El Capitan, and told Time Machine to backup. It got stuck on Preparing Backup for hours, so I stopped it, deleted the InProgress file, rebooted and tried again. After ~30 mins, Time Machine was still preparing. I looked into activity monitor and backupd had only read ~140Mb, in 30mins... Looking into iStatMenus, I find that backupd tends to have a read speed between nothing, and 120Kb/s (If I'm lucky. It sometimes peaks up to to 500kb/s, and very rarely 1Mb/s). Spotlight is not indexing (As I heard sometimes Spotlight gets in the way of backupd), and the hard drive has gone to sleep in the time that I wrote this, rarely waking up for my Mac to briefly read something from it.
Here's what comes up in the console when searching for backupd:
I'd rather not have to reformat my hard drive, in case I ever want to downgrade back to Yosemite, however I am willing to if it solves the issue.
Also, it seems like whenever I reboot my Mac, the hard drive loses its Time Machine icon, and reverts back to an orange drive.
Screenshot of Activity Monitor, Disk mode at ~50 min mark:
EDIT: I've tried disabling and reenabling Spotlight for the disk, and I have also wiped the .Spotlight-V100 folder and rebooted. No change.
EDIT 2: What seems to be some errors has appeared in the console
EDIT 3: After many, many hours, Time Machine has finished scanning and is now backing up! I'd still like to know why it took so long (I didn't expect updating to El Capitan to take so long. I excluded system files as well, although I guess I'm in for another long wait since I just removed them from the exceptions list)