The advantage is that, if you're in full recovery model and know how to do piecemeal restores, you can restore primary very, very fast (it's only the system tables) and then restore the critical application tables (if they're in their own filegroup) and then restore the less important table (if they're in their own filegroup), etc, etc

If it's just system in one filegroup and everything else in another, then it's not all that useful except as a starting point for further splitting.

No disadvantages.