the blessed API
Cocoa is the blessed API and it was before iOS was released. Java has been mostly irrelevant on the Mac for sometime and Apple's craptastic releases have been behind the curve. All this signals is that Apple is finally putting Java out of its misery and handing it off to someone else who will (hopefully) do a better job.
When OS X launched, there was a lot of buzz about Java applications with the whole "write once, run anywhere." This is before we all realized it was "write once, debug everywhere." The need and the strategy for Java, particularly in the application space, was aborted a long time ago.
As for the checkbox in Xcode, it's pretty clear that you haven't coded applications for either iOS or OS X. The differences aren't as simple as a checkbox. Let me repeat, for the umpteenth time, iOS and OS X are NOT converging. Are they going to have shared core libraries? Yes. Are they going to have ideas pass between one another? Yes. Are there going to be similarities? Yes.
Are they going to become one OS? No. Why? Because it makes absolutely, positively NO SENSE. I'm so looking forward to seeing 50% of the comments on this site degenerate into, "OS X IS DEAD! NETCRAFT CONFIRMS IT! iOS is taking over!" Every time any conspiracy theorist nutjob around here notices some similarity between the two.
It makes quite a lot of sense from a practical point of view for Apple to merge iOS and OS X back together, and their moves are all pointing in that direction so far - maintaining two separate OSs has been difficult for them (hence the last OS X release which was more housekeeping than anything else, with a price to match). I suspect we'll see the desktop become more like the phone OS in many ways (we've seen a preview of), and cocoa NSViews phased out in favour of UIView etc. Then there will be another blessed API - these things change all the time.
In fact what you're saying (sharing core libraries, UI ideas, being very similar) is very close to a merger, and could cover anything from the present situation to almost complete merging in everything but name. I agree there are certain differences in UI which are essential between desktop and phone, but that doesn't preclude having OS X move towards iOS, even to the point of being subsumed by it. That's no big deal, though it does indicate which direction Apple want to go in - more control over developers, mandating which tech developers use so they can't go cross platform, tying them in to their platform and making it difficult to port, and having one blessed API which is supported to the exclusion of all else.
These things are clear from their Mac App Store (at present optional) conditions, which mandate language, compiler, and toolchain - they basically tie you to working for Apple to improve their platform, and no others. Soon that won't be optional, it'll be required. Very like Microsoft in fact. The Java decision is mostly pragmatic, but ties in with other changes (app store) to indicate the direction Apple is headed - it's not a good direction for developers, or in the long term, users.
Oh noes! Look at the Windows 7 phone! Microsoft is abandoning teh PCS!
Actually, Apple are far more likely to abandon their Mac business (as they already partially have, than MS ever are to abandon Windows. Remember that line 'milk the mac for all its worth and then move on to the next big thing'? Jobs in particular sees Macs and the desktop as old-hat, and yesterday's war - there's a reason there have been no significant updates in desktop OS X for a while now, and the updates to Lion are mostly bringing features from iOS back to OS X - it is getting far less attention, and at some stage may be retired completely. Microsoft, in contrast, still earns most of their money from desktop OSs and the software that runs on them - everything else is just a way to guide people back to Windows.
