I don't know any apps that are geared directly for compatibility with PowerPoint, but I suppose what you can do is convert the PowerPoint documents into PDF, and use one of many apps that support PDF annotations.
With great reluctance because of the 9.99 price tag, I purchased the iAnnotate app. It's really a game changer in my opinion because of so many ways you can customize making it easier for you to make notes on. Underlining, crossing out, highlighting, adding note stickers is super easy. Honestly, for a productivity app that really lives up to what it claims, I highly recommend iAnnotate.
Separately, although NoteShelf is one of my favorite apps for digital handwriting, I tried just taking a screen shot and just pasting the image onto the notebook to add notes this way, but the quality of the images diminish to a great extent. So for annotating purposes,I can't recommend NoteShelf.