First of all, Time Machine sucks for backup. It's okay for version tracking, though. In general I don't trust any Apple-made solutions, I use their OS and that's it. I worked as Applecare support, so maybe I know something.
I use Carbon Copy Cloner --and there is also Super Duper-- for backups. These both make bootable exact clones, no games with symbolic links and not being able to find the real file like with Time Machine.
I have two backup presets. One is called Identical, which I use on drives the same size in case I would need to swap them in to replace my internal drive. it makes an exact copy of what is on my drive. So if I back up using Identical and then reboot from that drive there is no difference in content. I keep a few of these around, it would take maybe 20 minutes to swap that drive into my MacBookPro if the internal drive died. In this mode, if I delete it on my internal drive, it won't be on the backup.
The other preset I call Attic Mode, and it just keeps piling stuff up. So if I have a folder of photos on my desktop and back up, then move it to my Photos folder and back up again, that folder is in both places on that backup drive. This is done on purpose, in case bit rot makes a certain file unopenable. It also allows me to do roughly the same thing as Time Machine, and find something I deleted off my internal drive but which I had backed up at some point. For this I use a drive that is several times larger than the internal drive. It will also be bootable. When it fills up I get another larger one.
Another point of these bootable drives is that after backing up I can boot from one of them and run disk utilities on my internal drive to keep the directories healthy.