One challenge is marking up corrections that need to go back to the source document. I get proofs from a typesetter, and I need to mark it up for them to fix. I can't change the pdf text, because the typesetter won't see that. Acrobat's markup tools aren't terrible, but they aren't quite what I could do in the days of paper and red pencils. Unless I use the 'pencil' tool in Acrobat. I'd like to see that improved.