I think from a UI/UX perspective there is some room for improvement, but to answer your question they behave fundamentally different:

AI Chat/AI Assistant is more of a one-off interaction with an LLM

• so it's comparatively fast
• but the scope of the task is limited comparatively

Junie is our AI Agent - I like to think about it in a way that Idea and the LLM have more of an automated conversation till it comes to the best result for your original prompt

So, to your question, when to use what, I think patterns will manifest here more clearly over the next weeks and months but the way I use it:

• for simple tasks (generate a test, generate a method) => AI Assistant
• for broader scoped tasks (entire feature development, refactorings, tests for a complete feature, UI design etc) => Junie
• for explaining the current state of the software (functions, git commits, etc.) => AI Assistant

Both of them have their use case and noone get's phased our or similar, they both have different use cases with some overlay. I personally would like to see a more seamless integration (share context from AI Assistant with Junie) but those are things that based on the patterns identified over the next week we can polish and improve.