What this change does is to not allow developers to use 3rd party tools and libraries to create iPhone apps. One of the big benefits to using these 3rd party tools (other examples of these are MonoTouch, Unity3D and Corona) is that these libraries make it much easier to port apps from one platform to another because the "back end" code doesn't have to change significantly, you just need to recode the front end and interface for each platform.
And that's splendtacular, but you aren't going into what happens when middleware goes wrong. What happens when popular apps are developed with MonoTouch? It's all gravy now, but what happens in five or six years, when OS X develops in some way MonoTouch hadn't anticipated, or they don't update for whatever reason? Then all those killer apps become a millstone around Apple's neck, and they have to keep bending over backwards to support legacy technology. It already happened with Metrowerks' "PowerPlant" Integrated Development Environment. It was an extremely popular IDE, and a lot of great Mac programs were made with it. And then Mac OS X came along and PowerPlant didn't become compatible with it until 2004. The year after
Mac OS X had stopped being a futuristic, candy-coated curiosity and started being the main day-to-day OS for most Mac users. Bet that might've happened a bit faster if Apple didn't have to keep bending over backwards to keep new software on legacy frameworks running because somebody
couldn't get their middleware's shit together for five years.
There's a good deal of psychology at work here. Apple's had bad experiences with middleware, and they've had worse experiences with dependance on third-party software. I have four applications open all the time on my Mac, generally, no matter what else is going on: Safari, Mail, iChat, and iTunes. I can word-process in Pages, and presentation in Keynote. I can organize my photos in Aperture, and edit a film in Final Cut. These are all Apple-made programs. There was an Apple-brand equivalent for only one
of those programs ten years ago. That ecosystem didn't pop up by accident.
In fact, it creates the practical upshot that Microsoft, for instance, could stop developing software for the Mac tomorrow, and no one would necessarily have to give a shit. Compare that to 1997, before the IE bailout, when everyone was waiting for the hammer to fall on the Mac and Apple as a whole, when Microsoft would decide that the Macintosh market was no longer large enough to be worth the trouble and kill Office for Mac. Now, luckily for Apple, there was a democrat in office, and Microsoft preferred propping up the closest thing they had to a viable competitor to having Janet Reno and an anti-trust team start examining their collective rectums with a dental pick.
Things could've just as easily gone the other way. If Linux was a little more popular, if there was a more business-friendly Justice Department at the time, if Bill Gates just decided he didn't give a fuck about keeping Microsoft in one piece, Apple would be long dead and gone.
But they survived, and here we are, thirteen years later, in a world where Apple writes its own damn core application suites, and has its own damn IDE, and can thus survive perfectly well even if everyone else on the planet decides to stop developing for their platforms. Now, there's a lot of merit to a cross-platform approach. As an old-time Mac guy (hell, as a modern Mac guy), I definitely appreciate the merit of fostering development for minority platforms. But Apple will not
submit the survival of its products and platforms to third parties again. Saying they should is probably going to go over about as well as trying to convince gulf-coast fishermen they should vote for candidates who will reduce burdensome government regulation of industry.
Hell, you can even sell
web apps, and in a convenient centralized location once someone realizes there's an untapped goldmine and makes a Web-App Store.
And contrary to what you said earlier, Apple has nothing against web apps. They love web apps. Safari and MobileSafari play well with web apps. So if you want to develop something that'll run on multiple platforms with a minimum of per-platform individualization, make a damn web app.