the main problem with the web
is that you don't have a control from A to Z. You have to target some browers and sometimes even an OS. Not sure that a Flash/Flex app behaves in the same way on a Mac and a Windows.
The fragmentation arranges nothing, but in the first place you don't control the client and that's the problem.
Adobe is giving for free the development side, that's very appealing but you're still dependant to his player plus how is it handled by the various browsers.
If you want to cope with AJAX, you just have to take in account the browsers and the OS
So, what do you choose ?