When /var was created, people took everything in /usr that got written to and just threw it all into one filesystem. After that, /var became the place that you put anything (besides config files and the like) that needed to change or be written to, regardless of why.

The problem is that /var has wound up with two very distinct sorts of data in it: private program data and public data. Private program data is the entire collection of caches, databases, and other tracking information that various programs use to do their jobs. Public data is everything that users and sysadmins create and look at, with things like /var/mail, /var/log, user crontabs, and so on. (On some systems this may include web pages, SQL databases, and more.)

This matters because the two have very different importances and need very different sorts of handling for things like backups and operating system upgrades. Fundamentally, you don't care about private program data as long as the program works right and you probably actively want to not preserve it when you do things like reinstall the system or roll back to a previous system snapshot. However, you absolutely must preserve public data when you do things like reinstall the system.

That the two sorts of data are aggressively commingled in /var causes all sorts of practical problems for system management. Effectively, /var has been turned into both a system filesystem and user filesystem, and the two generally require very different and conflicting treatment. Attempts to patch this up in software are awkward.

(For example, Sun's Live Upgrade stuff goes to all sorts of contortions to try to copy some bits of your public data between various copies and snapshots of your system's /var.)

The obvious solution is to split /var into two filesystems, one for each sort of data. Unfortunately, changing Unix filesystem habits is a lot of work (and work that really needs to be done by Unix vendors in order for it to stick).