If you're using small backup medias, like cd-r, usb or similar, then it would be good to have system, apps etc on separate partition than rest of the data. It's easier to backup the whole small partition than start selecting what's needed to backup and what's not.
And I wouldn't want to have caches, temp files, downloads etc fragmenting my system and utils partitions. Or in worst cases breaking them.
And with separate partitions it's easier to have multiboot system.
And if you're using old FFS filesystem, the usual validating time is shorter for smaller partitions. Fixing and recovering FFS partitions also work only partitions under 2GB size and which are inside the first 4GB area, so I'd keep important data on small partitions inside those limits. And if you have to fix, check, defragment, recover data, then it's faster if you don't have to scan whole disk, which is really slow on Amiga.
And what's most important in most Amiga systems, your boot partition must be under 2GB size and most partitions work best under 4GB area, so that makes it practically necessary to have at least 2 partitions.
