Powerpoint is designed for presenations so its template's have the appropriate screen/page ratios. Powerpoint has terrible special effects to distract from the content when you switch from page to page. Powerpoint is designed to create terrible charts by people who know nothing about how charts should be created. All they care about does it look colorful.
An InDesign to PDF presentation has to be initially setup, but after that there is no worthwhile difference. If you want to create terrible special effects, you can but it takes more effort. If you want to create terrible charts you can. But you have to consciously create your graphics and special effects. In the end what you present is what you create. Nothing is leading you to do a bad job. [Do you get the idea I don't like PP Presentations:See Tufte's The Cognitive Sylte of Powerpoint: Pitching Out Corrupts within).
With a PDF file you can distribute our presentation to people who were there and they can see them the way you designed it to be seen. You won't have to worry about your font choices. You can include video and audio if you desire. People that do not know about or are not comfortable with Acrobat/Reader will use PowerPoint, because it is what everyone else uses. Sort of like you cannot go wrong buying IBM computers.
PDF and PPT files can each do things which the others can't, and the same is true of the software:
- PDFs can include embedded video, Flash, etc. and have no enforced structures for creating new pages (slides).
- PPTs can use video but the file isn't embedded, so you must be careful about distributing it. Slide editing has quite strict rules on fonts, layouts etc.
- PDFs are generally smaller and can use higher-quality graphics (vector art, embedded fonts, etc.)
- PPTs have a larger range of inbuilt options for animation and page transitions (PDF has some support for basic animations, but not many).
- PowerPoint has a 'presenter view' - Acrobat does not (it can show the full-screen view on a secondary monitor, but has no interface for the presenter to refer to)
- PPT slides can have off-slide notes that can be included on the printed layouts, PDFs cannot.
- PDFs rely on embedded fonts so are rendered the same on any machine, PPTs tend to replace fonts and that can lead to text reflow and alignment problems.
- PPT has a mountain of quick-start features (layouts, themes, etc.) to make a basic presentation very easily, but customizing the slides can be a pain if you don't want to follow the rules.
Note that the basic PgUp/PgDown/arrow navigation works the same in a full-screen PDF and a PPT show, so most presenter remote control "mice" will work, but the advanced versions which allow on-screen drawing etc. tie in to features which are only found on PPT.