plinden
macrumors 601
Base - similar in capabilities to today's mini, but somewhat larger to allow for a 3.5" hard drive and an LP PCIe graphics card. Add an eSATA port to the back. Front panel USB ports and 12-in-1 memory card reader (or side panel).
Hub - Exactly the same size/style box, connects to Base with eSata and USB. Has space for 2 user replaceable 3.5" SATA drives - comes with 1 or 2 drives. Has extra USB ports, maybe the card reader is here and not in the base. Has 3 additional eSATA output ports on the back.
Storage - Exactly the same size box (but could be thinner). Holds one or two 3.5" SATA drives. Connects to 2 of the eSATA ports on the hub. (Or, perhaps the Hub supplies power, so the storage connects to the nub through a special cable or docking connector.)
Not quite as good as you're suggesting, but the Newertech Ministack and LaCie Mini drive and hub (only one drive in each of those) are designed to fit in with the Mac Mini and they're not too much more expensive than standard external drives, and add firewire and USB connections. Two of those could be stacked under a Mini.