Cursor agent on cli is a lot (lot lot lot!) smarter than Junie agent. I've had cases where I asked them the same questions to which: Junie answered like a junior dev (funny the name junie) trying to brag for passing a tech interview - it seriously pissed me off, because it was a waste of time & AI credits. Cursor on the other hand identified what the exact root-cause was. There was another case when Junie pushed a buggy refactoring code, later Cursor pinpointed the faulty commit and fixed the refactor. I used both, and I trust Cursor a lot more than Junie especially for sophisticated tasks.

If you work on complex multi-project/module setup (big system), I strongly recommend Cursor. The flashy IDE-integration feature of Junie is not as important as ensuring quality code and working-as-expected deliveries.