I quite agree and all my big boxes have the system and data components on different drives (actually a lot of the common data is on a RAID 1 physically separate fileserver).
But for systems that only allow one physical hard drive, like the Mac Mini and laptops, at least separating data from the system on different partitions is cleaner than lumping it all together (and, as you say, makes re-imaging or restoring a system much easier).
Cheers!
PS: And the fileserver rsyncs periodically to another fileserver at some distance which maintains daily, weekly and monthly backups on (of course) separate physical drives. FreeNAS -
FreeNAS - Wikipedia, the free encyclopedia - how I love it!