From User Point of View
Seamless iCloud synchronization of apps preferences, at least the system ones like Mail.app
I have a pair of notebooks and sometimes I have to switch between them. One thing I find really tedious is tweaking the preferences, so they match your workflow on the previous machine. Finder, Mail, Xcode... in my case preferences are always out of sync, because I change my mind from time to time.
Seamless iCloud synchronization of the Dock
There is a famous Henri Ford' saying “If I had asked people what they wanted, they would have said faster horses.”. For now I am just asking about better Dock. This concept could change dramatically in the next major OS X release, but for now iCloud synchronization of its items would be enough.
Seamless iCloud synchronization of the Keychain
Ok, this thing is so obvious, I can hardly believe it's not already implemented in Mountain Lion. The only fact that conciliates me about this unimplemented feature is current iCloud state is a mess: one can't build a reliable system from completely broken components.
Better Finder' AirDrop
Sometimes it's convenient to transfer files within your local network using AirDrop. One thing that bothers me about this feature is its requirement for both parties simultaneously entering "AirDrop" mode in their Finders. If both MacBooks are mine and they stand on the same table I have to click too many times to simply transfer file from one Mac to another. Synchronization across the Web would be nice to have too. Btw, now I simply use Dropbox.
Silent update of the Mac App Store applications
Why for the God's sake we have to manually trigger the app updates and enter passwords again and again? For what reason password is mandatory? For a person who have many apps installed on their Mac this recurring process becomes maddening.
From Developer Point of View
Remove, or at least deprecate the obsolete NSButton types and styles
Why to keep these utterly obsolete button styles, if nobody is going/allowed by HIG to use them? Beveled buttons, square ones... wipe them out from the IB and UIKit, we don't need broken blocks in our LEGOs.
Completely get rid of NSCell class
Born for performance improvement this class is superfluous in 2013. NSCell introduces incredible mess in control customization. The idea to customize anything through the inheritance is questionable by itself and NSCell/NSControl pairing makes it close to impossible.
Give us standard tabs control like in Safari and Xcode
It's impossible to understand why this still didn't happen. Apple seems to be using the same control in Safari and Xcode for a couple of years already, though developers are not able to benefit from it too. Building your own tabs control is a time consuming task and existing solutions like ChromeTabs just don't feel native enough.
Fix File Coordination
I love the idea of file coordination, introduced in Lion. Possibly, it is the only sane way to serialize access to filesystem in user-space. The sad thing is it's half baked, buggy and not mandatory for anyone to implement. Apple pretty successfully addressed concurrency problem with Grand Central Dispatch. It made our lives easier with introduction of Automated Reference Counting. Could file coordination be turned into a real working solution to file system concurrent access problem? I hope so.
Fix Interface Builder Auto Layout support
To put it mildly, Interface Builder and Auto Layout didn't play well together. I really love Auto Layout by itself (though I permanently still have problems with it). The API is clever and innovative, it amuses me how it was been retrofitted into the aged AppKit. Long ago I stopped fighting the IB and begin to layout simple views in code. I still configure leaf-views in IB, but then programmatically setup their dependancies in code using constraints.
Innovation in language design
During the last years numerous developers turned to the functional programming languages feared by unmanageable mutable program state in multithreaded environments. Brightest GitHub guys released awesome and highly innovative ReactiveCocoa framework implementing Functional Reactive Programming (FRP) paradigm, that I my opinion conciliates both worlds: imperative and functional. Unfortunately, to this stuff be completely usable it should be universally embedded in the Cocoa.