Hi! I know this is two years old, but I needed to do this today and stumbled on your post. Since it only had half the answer, I thought I’d contribute the rest of my solution.
I exported from Powerpoint as PDF.
Imported PDF to Illustrator, 1 page at a time.
For each page, I separated each sublayer onto its own layer.
Save each page as it’s own Illustrator file.
Import as composition in After Effects to retain layers.
Unfortunately importing directly into Premiere does not retain Illustrator layers.
If anybody knows an easier way, or a way to get layered powerpoints into Premiere, I’d love to hear it.