I've done alot of work with Flash as an application medium and am pretty quick to defend Flash in this capacity. That said , there are certain basic limitations to the Flash player and VM that preclude a large range of applications otherwise viable as RIA/LIA/.. implementations - IF you use flash alone.
For instance the MX player still isn't very efficient in parsing and handling XML , and doesn't handle documents in memory very well.
HTML presentation is limited , you can't navigate an imported HTML doc if is isn't xhtml.
You can't establish a secure socket connection directly.
There's no direct access to memory and you have to roll your own task scheduling methods.
I think that the best route is hybridize the development of such apps using Flash and a container environment ( the browser , an HTA , C++/VB wrapper ). This method exploits Flash's strengths as a UI layer and interactive visualization medium while providing a more robust alternative runtime for offloading certain computation and memory intensive tasks. It's alot like the concept of hard & soft layer development.