It is almost certainly based on the Cortex A9 instead of the A8 that current Snapdragons use, which means multiple cores. Apple knows how to use multiple cores effectively and the ability to stop them when not using them is a nice power savings.
Snapdragons extend by adding in the wireless circuitry. I'd wager that A4 left that to other chips and extended with someone's graphic rendering engine, say Imagination Technologies?
But I think the most important reason is that it lets Apple make the design decisions that make sense for their projected use, not what some chip house thinks will be the focus three years down the road.
The Snapdragon and Cortex A8 are both implementations of the ARM V7A architecture, but are completely separate designs. The Snapdragon is Qualcomm's version and is unique to Qualcomm, whereas the Cortex A8 is licensed by ARM to third parties.
It's the same as Intel and AMD both making x86 chips; the ISA is the same but the design is different. However, ARM is more than happy to let Qualcomm design thier own.
I thought Cortex A8 was TI's implementation of ARMv7 and Snapdragon Qualcomm's: the ISAs are the same but Snapdragon can run distinct cores at distinct speeds because of disjoint caches per core, beneficial for power savings, for example.
Snapdragons extend by adding in the wireless circuitry. I'd wager that A4 left that to other chips and extended with someone's graphic rendering engine, say Imagination Technologies?
But I think the most important reason is that it lets Apple make the design decisions that make sense for their projected use, not what some chip house thinks will be the focus three years down the road.