After a brief exchange about Daring Fireball's article on the matter, Greg Slepak wrote:
I still think it undermines Apple. You didn’t need this clause to get to where you are now with the iPhone’s market share, adding it just makes people lose respect for you and run for the hills, as a commenter to that article stated:
[...] I don’t think Apple has much to gain with 3.3.1, quite the opposite actually.
To which Jobs sent (not iPhone or iPad this time, but from his Mac):
We’ve been there before, and intermediate layers between the platform and the developer ultimately produces sub-standard apps and hinders the progress of the platform.
That users are picking sides is interesting. Adobe wants to control the creation and distribution tools (Flash CS5 and the Flash plugin). Apple wants to control the creation and distribution tools (Xcode and App Store). There's a battle going on for the next generation of computing, with Google, Microsoft (who won the last one) and others deep in the mix and they all want desperately to win. Both are good or evil depending on how closely their goals mirror the individual's in question. So, while picking sides is inevitable for some, it's also part of each company's strategy.