What kind of finished product can I make?

What do yuu mean by 'quiz in the middle of the animation'? What output format will you use from AE? Probably H264 which is a video format? When inserting the video as slide video, you can convert it to an interactive video. It is possible to insert Knowledge Check slides in an interactive video and content overlay slides, but not normal quiz slides to be tracked in a LMS. In that case you will have to use separate quiz slides, not in between the video. 

Captivate has a few different output options and which one you choose really depends how you are going to deliver your content to end users. However, nowadays Flash output is not recommended and since PDF output relies on the Flash player plugin being installed on end user systems, it's not recommended either.

That leaves either publishing for an APP or HTML5.  The latter is almost certainly going to be the best option because getting apps to work and be delivered to end users (or tracked on an LMS) is way too complex.