Isn't that exactly what iOS and Android are though? I mean most of the criticisms of iOS are against Apple's obsessive curation of it's simplicity and usability, and it 'came to power' smack in the middle of the internet age. People are always complaining that native apps for internet services are a threat to the web. It seems to be exactly the thing you're saying the web makes impossible.
Apple even release a web framework for making sites that looked and behaved as if it was native to iPhone.
Only after the jailbreakers enabled third parties to fool around with the guts did we see apps happen. And initially Jobs wants to sue those app devs and distributors into oblivion.
Yes, Jobs did a song-and-dance about web apps but not because they didn't want 3rd party apps but because Apple wasn't ready to support developers on what was a new platform. Apple plays it safe.
For one, it's not consistent with the timeline and secondly as the jailbreakers discovered there was quite a bit of infrastructure to support apps even in iPhone OS 1.0.
* iPhone release date: June 29, 2007
* iOS SDK Announced: October 17, 2007
* iOS SDK Released: March 6, 2008
* iPhone OS 2.0 release date: July 11, 2008
Apple had such a tough time providing enough support to developers that they restricted access to the paid developer program to just 4000 (Apple said 25000 tried to join).
There wasn't enough time for everything to happen (including relatively sophisticated tools like the iPhone Simulator) if it was just a reaction to jailbreaking.