I've been testing Catalyst extensively over the past couple of weeks. I have a whole Application UI design built out at this point... probably something close to 100 screens (using custom components to manage groups of states to keep things manageable).
Anway, I've come across a few things:
1. When publishing to a swf, Font Embedding doesn't work. I'm pretty much stuck with the default fonts.
2. You can't rearrange layer folders. I can move items and groups withing and between folders, but I can't move the folders. This is frustrating.
3. I've encountered a bug occassionally when copying graphics in from Illustrator. If you flatten text when copying the graphics in, sometimes Catalyst will mistake the copied object for an existing object. It's difficult to explain. Try copying a bunch of different objects from AI to Catalyst, make sure they have text and flatten the text. Try deleting some of these in catalyst then importing other graphics containing text from AI. It may be difficult to reproduce this bug.
4. If you save, then Publish to SWF and then quit Catalyst, you will be prompted to save. However, if you choose to save at this point Catalyst will take several minutes to save or even lock up (at least in OSX Leopard).
In building out such a large project I've had an opportunity to explore several workflows. Our Interaction Design team usually wireframes in AI and we lay out all of the screens sequentially (these typically go into powerpoint decks so we need both the sequential views as well as the transition animations and UI demos). That doesn't fit with the recommended layer comp practice. However I've found that starting from a new Catalyst file and copying the graphics in from AI as I need them works fine (aside from the bug I menitioned above, #2). One thing I have't tried yet, but that I think would be helpful (especially since I also know Flex and later import the project in Flash Builder) is to skin a button that has several instances in the UI design and then using instances of the skinned button in Catalyst rather than converting each separate button into a new skin. This keeps things more manageable in Flash Builder. I have way too many buttons in my components directory when I really only have a handful of distinct buttons in my design.
Since I have so many screens, I'm using custom components to break up the UI into more manageable sections (this is actually more ideal for a Flash Builder import as well). One thing that would be really helpful is having an event for custom components that can fire when entering the component's default state. For example I have a 'home screen' where i have my primary set of states. Each of these states contains a custom component. When transitioning from the home screen to one of these states I'd like to be able to fire an event from withing the custom component. I've found a work around where I can use a mouse down event on the button press initiates the transtion between states that then makes the mouse up available once I enter the next state (now within a custom component).
The incorporation of swfs is really convenient. One thing that's missing is the ability to dispatch an event when the animation completes. It actually be really convenient to place an "Add Interaction" action on the timeline from which you can Play Transition to State (or any of the other typical options). That way I could create a progress bar animation in Flash, import the swf and then branch off from the animation at different time periods to simulate longer or shorter wait times at various points in an application.
Also, I'm sure this has been mentioned a million times, but you really need to get round tripping between Catalyst and Flash Builder working at some point. I need to add code in Flash Builder since I design primarly for touch screen applications so I need to add code for direct manipulation of lists and other scrollable components in Flash Builder, then I have to keep copying and pasting this code back in after each iteration in Catalyst. Would be great if I could just loop it all back through Catalyst.
One other thing... and maybe this is a better topic for the Flex forum, when importing an FXP file in Flash Builder it would be really nice to have the option to create an Air applicaiton. Currently that option isn't available so I have to create a new Air application then copy the code in from the FXP import.