I read your suggestions with interest. Express Animate is a free program and I would have to think of the time (cost) of implementing changes for any perceived benefit. I came to the program looking for a one-off solution to a personal project and was impressed, it did exactly what I'd hoped. I spent time exploring each option and discovering possibilities, and was inspired to try more. I can see that it is limited in comparison to professional programs yet I usually managed to work out whatever effects I wanted to achieve. I've sometimes laboured over something that another program might deliver at a click but really I've no complaints. A great product, and getting better.
About your ideas:
1. Earlier versions of Express Animate had a tabbed Object panel, similar to your thumbnails suggestion, that perhaps took up too much space. I agree with obtusity, that giving your compositions meaningful names should allow you to recognise every composition and switch between them to work on each individually. I don't know what would be the benefit of seeing compositions in thumbnails.
It would be useful to know which assets have been used in particular compositions as it's easy to make changes in a composition that might be unwanted where it's used as a nested composition in others, and since these might have different names or be used as copies, things can get complicated. Where I use a drive to switch between different computers I frequently have to change File Source paths, so I need to find what has been used, and where. Not a biggie.
I would sometimes want to reorder items in the Object panel, for example in order of appearance in the timeline instead of stack order the same as the Composition panel. It might be useful to group by object type, and this could be achieved by right clicking an object's icon.
2. I'm not sure what you're after here. When you go to New Object you see Clipart Image and Clipart Sound or you can click the Object tab to get icons for Clipart Library and Sound Library. Each opens a window listing items as you want. What could be more intuitive and easier to navigate?
I've found that if you preview sounds they are saved to a (hidden) folder on your drive so become available offline.
3. Photoshop is a professional program and the Puppet tool has a specialist use. I've seen it in After Effects. I think possibly because of the name, some will approach Express Animate as a tool for making animations above being a motion graphics editor. There are other better tools for this and some are even free.
4. Just a personal thing, but I find 97.8% of all clipart completely useless.
If you've used After Effects then you know what would be the ideal. For anyone thinking of more than just an occasional motion graphics project or exploring beyond recreational use then this kind of professional tool would be the way to go. I'm happy where I am.
My wish list:
1. Set fill to None
Draw an L by clicking three points and Express Animate gives you a filled triangle, with closed path, so there is no way to create line drawings. I spent a lot of time when I started trying every option because I thought I must be missing something. I've since found ways to render the effect but no Stroke/Fill is a severe limitation. Trim Paths would be a dream.
2. Import SVGs
After Effects is perfectly integrated with Illustrator. Might Express Animate make similar use of open source Inkscape?
3. Open more than one project
I'd love to import compositions or at least copy and paste objects between different projects. Yes, you can render a scene and import that, but then there is no way to work on it, and I often have to reinvent the wheel for an effect when starting a new project.
5. Convert text to objects
6. Region select for Real-time playback
It's easy enough to set the Start position but you have to guess where to Stop because during caching the Timeline ruler remains static. Now try adding a few seconds to either beginning or end! Might it be done with bookmarks?
7. Zoom to area
Like every other app.