For me the biggest disadvantage is the somewhat closed system. Sure, I can strip the DRM off my books and I can convert books I got elsewhere to read on the Kindle but I'd rather it all just worked. Most Kindle owners probably don't know they can do this or are intimidated by the process so it is a closed system for them.
I would add one disadvantage for the Kindle for PC that cathyhk didn't mention: you can't search. That is so annoying. As for PowerPoint, you can convert that yourself, no?
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