I would hate to blow it out of proportions but for me the difference is huge. I think the 908 is a bit 'tame'. IE you can actually catch the tail end if you are stupid with the throttle. However for me it lacks that Razors edge, on rails feeling that a proper race car should provide. The 787B feels like it will dive blindly towards apexes regardless of whether the car has enough grip to make it through the corner. It will do whatever you tell it to do, right or wrong (I'm a huge fan of this feeling).
Secondly, the car is just cooler. The history behind the Mazda win at Le Mans is fantastic. The car's design is both visually beautiful as well as efficient.
Lastly lets not forget that 4-rotor! The handling sells the car but the engine seals the deal. Besides having a fantastic power to weight ratio (better than the 908) it has much less torque. Which for me proves to make the car more predictable. You are punished less for indiscretions of the right foot.
But the best part, by far is the sound. Not just that it is roaring and raw, but that as the engine makes its way into the redline the sound changes completely. From a harmonious soaring rev, to a much more savage tone. It almost sounds as if the engine is edging closer and closer to its own event-horizon. which makes gear changes simple... when it sounds like the engine is going to become a black hole, you shift up.
I dunnno for me a car has to be more than just fast, and on that note the 787B delivers.
(if I had to do it over again I wouldn't buy the 908, I'd go for the 787 then the R8-01)