The Apollo had quite a bit faster access to the custom chipset (even better than many '030 cards), which was ideal for demanding AGA demos, and made the system feel a bit snappier in general. HD access as far as internal IDE was faster with the Apollo, but ofc the Blizzard had a much much better SCSI option.
The fast chipset access apparently caused compatibility problems with some motherboards (not unlike the ACA), which could be remedied by the usual timing fixes. Outside of that, I had mine running at 80MHz for days on end without crashing, and it worked fine with all my clockport cards (unlike the Blizz). The only thing I preferred WRT my Blizzard 1260 was the ability to take more RAM, but with the CPU facing down (it's up on the Apollo), keeping the trapdoor on wasn't really an option.
BTW - If you do a search over at eab in the hardware section, you'll find a thread from a few years back with a bunch of bustest results.
