The problem really is that most of the innovation is now occurring on iOS rather than OS X, with OS X mostly just getting ported iOS features.
Now, I don't have a big problem with this, as iOS, being a mobile platform, is where innovation really shines as it needs to marry all the best new features with strong performance.
Where I see Apple falling down is that they're not doing enough to make these ported iOS features desktop friendly. In particular many of the features are over-simplified, which might be fine on a more limited platform, but on good laptops and desktops it's resulting in features that are prettier than they are function.
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Aside from all this, the Finder still could use a major rethink; aside from adding tabs to the current Finder, I can't help but think that Apple's innovation could be applied to creating a new method of browsing the file-system that's more streamlined, or at least less buggy and inconsistent. Considering it's such a commonly used part of the OS, it really does get overlooked; I'd pay for an OS update for nothing but a Finder upgrade, if it was good enough.
No there is just as much innovation coming from OS X. Apple doesn't highlight these features because often they are seemingly small and insignificant but they form underlaying tools that make software or the performance better.
Everything you mentioned here is the window dressing stuff. It's the features that Apple tells consumers about. When talking about innovation you have to take a holistic view. Innovation from a consumer standpoint is different than innovation from a development standpoint. Consumers need to see UI innovation like Mission Control and Full Screen. Developers need to see UX improvements like the API behind Share Sheets or a better way to access filesystem data.
%80 of the time here on MR the person screaming about innovation is in the consumer camp. If something doesn't beep and flash at them they are bored. Hang around in developer circles and you get a different perspective about the worthiness of an OS X upgrade. Lion was bad from my recollection and I'm waiting for more fleshed out Dev Betas before we really understand how ML has progressed from a development standpoint.