Complex presentation slides: Powerpoint (or its alternatives) and Latex

This may focus on academic slides but those with presentation with complex setup, please feel free to share your thoughts. For equation heavy talks plus diagram heavy layout (arrows left right, boxes, callouts), do you still build everything in PowerPoint, or do you prefer LaTeX Beamer?

Also do you ever do a two step process: make the equations and core layout in LaTeX, export to PDF, then add arrows and boxes on top in PowerPoint or another tool? If yes, what tool and what export settings work best?