It's worth noting that Adobe is very reluctant to deprecate API's. They've historically preferred (with AVM1/AVM2) bundling new VM's into the player over deprecating features. And any deprecation must be version-specific, and tends to be more for API consistency than anything else.
What really disappoints me is Adobe's reluctance to support really neat Labs projects like Alchemy. Want to run C (or any language which compiles to C, like haskell!) in the browser? It's been possible since Flash 9, way before NaCl. Official support is coming soon but it's a bit too bad it took so long.