Apple's introduced restrictions on original programming language, which has been considered an attack against Adobe Flash. However, there is more to it. The market for smartphones has been very diverse for a long time. Microsoft has attempted to standardize smartphones on Windows Mobile, which failed because of its power consumption and because it was always a bit late to the market. Apple made a huge hit with the iPhone, because they combined new technologies that made it possible to give a great smartphone experience, earlier than what would otherwise have been possible. They were rewarded for innovation.
Now, that everybody is catching up on the basic technology, like touchscreens and sensors, other software vendors are seeking ways to standardize the ways that software is written for many platforms. There is a huge saving if software vendors can create one application that can be deployed on iPhone, Android, Maemo, Bada and others, and on many different form factors. What would the result be for Apple? They would just be one of many, and they would probably not have any significant advantage over the competition. This means that their margins would drop, in a market where prices are already going down, and they would earn a lot less money. Apple does not want that, of course.
For the consumer, that would mean a lot of apps, which do not exploit each platform well - the feature lists would focus on the lowest common denominator for the target platforms, and few platform-specific features would be used for marketing apps. It would be hard for phone platform developers to add new capabilities that the developers would love to use.
Apple's strategy is to separate itself from the apps on other platforms, giving the user a unique and different experience, which they believe will be better than usual. If you have three features, and Apple does the first two perfectly but not the third, and the competitors do all three in a mediocre way, many consumers will pick the Apple product. A good example is the HP Slate: It supports flash, but nobody cares, consumers still want the iPad.
The iPhone and the iPad will never become devices that can do everything. Of those who had this expectation, many will be unhappy about Apple's latest move, but anyone who wants innovation in smartphones, great user experiences and real choice, should be happy about the new section 3.3.1.