My guess is that CryEngine3 is mainly targeted at consoles, but it will work as their PC engine too, and that's what they will market and license to all developers.
They probably optimized CryEngine 2 so it's able to run on consoles (low RAM) but added any new effects and extensions they've developed since 2007, similar to how the Crisis Warhead engine was a modification of the original Crysis engine, and decided to call it CryEngine 3. So, overall it's only a small upgrade from CryEngine 2.
And in some future PC exclusives we'll probably hear some developers say "we used a modified version of CryEngine 3 that wouldn't be able to run on consoles".