Depends on what is on the Nubus card. If you decided to make a processor on a card with video/memory/HD interface then you only need the Nubus slot for power and I/O which is low bandwidth anyway. Asuming all that stuff will not fit or uses too much power you just daisy chain multiple cards to each other and not send all that data over the Nubus slot (kind of like DSP cards attached to Video capture cards).

PDS cards are great if you intend to keep using the machines built in CPU, but are limiting since you have to tailor each card to the CPU speed (different PDS sockets) and varying RAM speeds plus there are plenty of machines without PDS slots (840av, IIx, IIfx, IIcx, IIfx and its oddball non working PDS, etc).

These days something like a super computer on a Nubus card would be cool (Radius Rocket on crack).