I too have built a reasonably sized Angular app in the last year [1] and echo a lot of these thoughts. I'll add a few of mine:
1. For CSS, honestly for any project it'd be hard for me not to simply use Bootstrap and be done with it and then do the minimum CSS possible (I say this as someone who has been doing CSS for years). Bootstrap really is the de facto CSS for the modern Web;
2. Organization: I agree the angular-seed project (which I started with and still use) isn't suited to organizing large projects and I agree separating into functional modules is the way to go;
3. Directives are awesome but to get all the two way data binding working requires a fairly deep understanding of how they work (to get the correct combination of scopes, transclusion, etc);