My picks are Extensibility, including widgets and inter-app communication, Continuity, HomeKit and Swift. Overall, while it's true Android users like myself have had many of these features for at least a couple of years, you cannot deny Apple's smooth implementation. But I will leave that debate for another day.
Another take away is the evident cultural change at Apple. The jokes were actually good, natural, not forced and Hair Force One is turning out to be Apple's public number two; he carried the keynote with aplomb. More importantly for developers, Apple is letting them into its walled garden albeit not completely.