The M9 will have full integration with the main CPU courses. Now that it has moved onto the main processor, there are still a lot of questions. Chipworks' Dick James thought from the die shot that the M9 looked like it was in the same package, but not on the same die. That would make it a System In Package type solution like the Apple Watch has. If that is the case, there's a fair chance it's still an NXP design. If it's on die, I would say both possibilities should be entertained - it's a licensed NXP design or an Apple custom one integrated into the die. The CPU already manages low power states and small bursts of light activity, so that should fit right in with what the M9 wants to do.
Motorola integrated an always-on listening process first with the Moto X, and they likely had more tolerance to some small amount of current for the process because they have a bigger battery. I'm sure that moving it on chip saves them power (in addition to PCB complexity and space).
Optimizing power and other aspects of the RF chain is only going to get more popular. Analog/RF circuitry is hard to do well, so Apple has to take their time if they are working on a custom solution.
Likely 2GB. Some people seem to have picked up on
this story of it having 2GB, but the detail isn't explained at all so I think it's more likely a typo. (
Edit: looks like there's another, more credible source now
https://www.reddit.com/r/apple/comments/3ka86y/no_mention_of_ram_in_new_iphone_or_ipad_pro/cuwb6sz)
The most likely reason I think it has 2GB, other than the rumors from reliable sources before the reveal, is actually related to the game tech demo they did on the iPhone. When they were gleefully listed the new effects they could add, the first one they mentioned was "high resolution textures." In the gaming world, high resolution textures are resources-speak for RAM intensive. If they're able to do higher resolution textures than they were before, it's likely because they have a bigger pool of RAM to play with.