Export from After Effects, resave with QuickTime, import with PowerPoint
Alec Jacobson
June 23, 2011
My ridiculous regimen for creating small video files that Powerpoint knows how to play:
  - Render from After Effects using Best Settings, Animation, Loseless: this makes a large .mov file
 
  - Open in QuickTime and save as HD 480p, HD 720p, or HD 1080p (the largest available), this makes a new, small .mov file
 
  - Drag this new .mov file into PowerPoint: often PowerPoint screws up the right most column of pixels on the preview image so I have to cover that with a small white rectangle