'The biggest flaw in the Flash IDE is that it basically encourages bad code, you can bury code in a literally infinite number of places - external files, movie clips, timeline frames, frames within movie clips. It gets ugly very fast.'
ActionScript developers do not use the Flash IDE for coding. Designers and casual Flash users use the Flash IDE. It's not meant for development. Flex Builder is Adobe's provided IDE for ActionScript and MXML development, or as an alternative, the Eclipse FDT plugin. Ideally, you shouldn't write any code in the IDE, and you certainly shouldn't be putting any in movie clips (apart from the odd stop).
'There is no frame-based animation, so it works more the way programmers are accustomed to working - with a collection of files compiled into a finished app.'
Surely this is no different to AS code ? You write your classes and you compile them to an SWF ?
'WPF also lets you define the start and end conditions and can automatically calculate the movement for you.'
In Flash, this is called a tween, it can change any property of any object over time (yes, seconds or frames) and it can allows custom 'easing' functions to create non-linear movement. Tweens can be completely written and controlled by code, with no interaction with timelines required.
'WPF "just works," and can save you tremendous amounts of time. Animating the opening of images in our slideshow app, for example, required just ten lines of code cut and pasted straight from the documentation.'
If by 'Animating the opening of images' you mean they swoop in to view, or scale up etc, this is a single line of code in AS.
I'm not saying that Silverlight doesn't have some obvious advantages, it does, and these are well described here, but I feel the authors knowledge of Flash development is somewhat lacking, and as an ActionScript developer myself, I feel a bit let down.