I'm running Acrobat 9 Std on Windows XP. I've noticed many times that when I load a PDF into Acrobat and select the reduce file size option, the amount of I/O and time taken to completion seems extraordinarily large. By far the longest part of the process is subsetting embedded fonts. For example, at the moment I have a file size reduction running on an 80 page 10Mb PDF. So far it has been running for about an hour, and Task Manager shows that Acrobat is using almost 600Mb of RAM, a fairly constant 55-60% of CPU, and I/O reads are over 10Gb and writes over 15Gb. The computer has 4Gb of memory and Acrobat is the only application running, so swapping is not the cause of the slowness. I have other larger manuals (some of them about 800 pages long) that I periodically need to run this process on, and those can take almost a day to complete the size reduction, with Acrobat reading and writing over 100Gb to complete the size reduction.
These manuals are all produced by running texi2pdf on the texinfo source (both HTML and PDF get produced from the one set of source files), so there is nothing I can do at PDF creation time about the size of the created files. I can usually achieve about a ~50% size reduction by running them through Acrobat, but the way that it does this seems extremely inefficient.