I want to make a presentation video (animation in After Effect or Flash) but can control it like power point (such as. adding shape then link it to another slides).
After Effects makes video, Flash (now Animate) makes interactive presentations. Video is not interactive but you can set up the timing to an audio track and it's easy to play on any device. Interactive presentations are harder to distribute to the public. There are apps and sites like YouTube that will let you add links and other limited interactive elements to videos.
It's your choice. Both apps have a steep learning curve. If you are new to both apps then expect to spend a couple of weeks learning how the apps work before you create much more than a simple move or two.