Connecting them will be as simple as a future software update. Amazon's challenge right now is to get the hardware in place before its competitors (Nest, Apple) - and it seems to be pressing hard to get a wide range of devices in every room of the house.
I agree with you on this, but generally they'd have an easier job of it if they worked as a connected mesh rather than independent controllers. I can't say for certain but it doesn't seem like the added engineering time would be that much greater.
