I mean, do you just want to say "These two PDFs are not the same" or do you want a detailed list of diffs? And do you want to compare their external appearance only, or do you want to treat two PDFs which appear the same to the user as different if their internal structures are different? And do you care about things which the user often doesn't see, like thumbnails?
I'm sure there's a lot more questions that could be asked. I think you need to work on your requirements specification a bit more before you start implementing.