I think I've read there that you shouldn't backup your system apps' data since it might mess things up.
I've read it's ok to backup your system data, that way if flashing your new ROM fails or you decide to go back to the old one, you can do a full restore of ALL data. You shouldn't restore system apps or data across different ROMS or different versions of the same ROM, you are ok to do so for the same version of the same ROM. (unless it was some corruption of that data that was causing problems)
Something to consider: Titanium Backup doesn't keep all your home screen icons, you'll have to rebuild your home screen layouts everytime you flash. Nova Launcher can back that up and save you that headache of trying to duplicate your home screens.
When I'm going to flash a new ROM, I uninstall any apps that I don't want on the phone anymore so they don't get backed up. Then I do a backup in Nova Launcher's settings to keep my home screen layout and finally back up all user apps and system data in Ti Backup. Do the system resets, wipe data and cache and flash new ROM. Reboot, install Ti Backup and restore ONLY user apps + data (NOT all apps + system data). Once my apps are back on the phone, I remove all widgets from the stock launcher screens so they aren't running in the background, set Nova launcher as my default launcher and go into Nova's settings and restore my home screens. The only thing I haven't figured out how to do yet is backup my custom ring tones and notifications.