When you’re trying to work out the best policy for backing up, you might instead find it easier to think about how you would use your backups to restore your Mac.
The whole purpose in backing up is to get you out of a hole. That hole might be a little one, when you discover that a critical document has gone missing, or your working copy lacks a load of changes that you made to it yesterday. Or that hole might be a yawning chasm when your Mac suddenly dies and has to go off for repair: you need to get a stand-in up and running fast, and can be fairly confident that when your Mac returns you will have to restore its internal disk from scratch.
So when you are working out what needs to be backed up, and how often, you should ask yourself what you would need when you come to restore a single file, or your whole system.
There was a time, not long ago, when a really neat way to do this was to keep a mirror image, or clone, copy of your startup disk, on an external drive. In any worst case scenario, all you then had to do was connect your new (or wiped) Mac to that copy, and copy it across in its entirety.
You may still be able to do that with certain Macs, but it has become far less dependable. One obstacle is the Fusion Drive: it is possible to wrangle your way around a Fusion Drive and get it to accept this sort of cloning, and Carbon Copy Cloner can do it. But some users find this complex and not reliable enough to use in their backup-restore plan. And reliability is very important.
Incrementally-updated mirror copies will also let you find lost documents, but cannot compete with the likes of Time Machine (or El Capitan’s versioning scheme) if you need to locate yesterday’s saved copy of an important file.
Generally speaking, the best way now to set up a new Mac, or a repaired and wiped old Mac, is to install El Capitan from scratch, then restore everything else that you need from a recent backup. If you try anything else, you could easily be left with fiddly problems which are a pain to fix.
So the next question is what do you want that backup to contain, so that you can restore from it?
Protected system files
For a start, there seems little or no point in it containing the El Capitan system files, particularly those which are protected by SIP. Those have to be installed by the El Capitan installer now, not from your backup. The snag is that there is no easy way to exclude them from Time Machine backups, for example.
Although most of the contents of /System/Library, some of /Library, and some hidden folders are protected by SIP and therefore should be excluded from backups, you cannot accomplish this by adding those folders to the list of those not backed up. This is because some files in them are not protected, and are written by user actions. Examples include some third-party drivers, extensions, and services.
This is a flaw in Time Machine which needs to be fixed: there is no point in it backing up files which it cannot restore, and SIP makes it practically impossible to restore much of the 10 GB used by /System/Library, for example.
Apps and others
You should take a careful look at your installed applications in /Applications too. If they are (almost) exclusively delivered and maintained by the App Store, then when you come to restore, it may be just as good to install them fresh from the App Store. If you have some key apps which are delivered and maintained by other services, then it is likely to be important that you do keep a full backup of /Applications.
Apply the same purposeful analysis to large files and libraries, such as iTunes Store movies. Do you really want to back them up, or would you be as happy downloading them again when you needed to?
One technique which I have long used for very large files, such as my own high-definition movies, is to store them within a single folder, and add that to the Time Machine exclude list. When I do want them backed up, because I have been modifying them, I can place them outside the excluded folder and obtain a snapshot.
iTunes music libraries are another area which merit careful consideration: if almost all your tracks are purchased from Apple, then you may not want to keep them backed up locally.
The other thought which must cross your mind is what you would do if you had to perform that ultimate restore, to a new or wiped Mac, but discovered that there was a problem with your Time Machine backup. Disks usually pick the worst possible time to fail, and that could be when you’re trying to get all your files reinstalled.
You may decide to couple Time Machine backups with less frequent mirroring of, say, just your Documents folder and user (login) keychain using Carbon Copy Cloner (or another utility). That should give you a second chance without incurring a lot of additional storage space or time spent maintaining it. Keep this on a completely independent device – its own external hard drive, perhaps – for safety.
Finally you should think carefully how often each of these backups should be made. Time Machine, with its automatic hourly backups, is great for anyone working on their Mac, where the cost of making up a couple of hours of lost work would be significant. If you are not doing that, and could afford only daily backups, then those could save a lot of space on your backup drive. You can use third-party Time Machine tools to adjust the frequency of its backups. I have always had slight reservations about these, as they don’t just tweak one of Time Machine’s settings, but have to take it over completely.
Hopefully this will have helped you think and plan more realistically, so that your backups are as efficient as possible, and designed to get you out of trouble.