A major difference is that while original Bluetooth used time-based channel hopping BLE uses sequence-based channel hopping. This means you don't have to keep your local clock or receiver running to know what channel to listen to, rather you listen on a given channel just before you want to speak/receive something and once something shows up there you know where you are in the sequence. BLE-only chips can basically be entirely powered off most of the time without losing connection, whereas bluetooth needs a running clock or a large receive window to stay connected.
Now that I write it out, I see that frequency hopping would count as a "higher layer," but I think it's still managed in hardware, which could be why there are many BLE-only chips. It's possible the GFSK parameters are also different, and of course the layers above the link manager are vastly different (for some reason).
https://en.wikipedia.org/wiki/Bluetooth_low_energy#Technical...