Well the cons you have listed far outweigh the pros in my opinion.
Back in the day when links were just a webmasterly thing to do this would have been a great tool. Today however with the advent of site ranking algorithms which in part consider linking practices, I don’t think it’s very beneficial tool
As you pointed out 99% (and that may be high) of the sites that you will exchange with will have a very low PR. Furthermore, good percentage of these sites wont even have the script set up correctly, so page 8 where you link is located wont even get crawled.
Nothing personal to anyone that uses it, but I have always stated this is a lazy mans tool and that taking the time to build your link partners manually will always be more beneficial to both individuals participating in a link exchange.
This may be getting off topic, but is related to the manual processes …
Of late I am getting more stringent when accepting link partners. I am putting more emphasis on the quality of my partners sites than I ever was. I have seen evidence that Google is beginning to place more weight on the quality not quantity of links both inbound and outbound.
Additionally, I am also interested in mutually beneficial link exchanges i.e. if I put a partner on a PR6 link page, I don’t want to be on their PR 2 link page.
So my opinion is much the same as Nikes old slogan JUST DO IT – manually that is!