What are your pet peeves about the tools? I have a lot. For example, pt-table-sync doesn’t let me do things I want it to do sometimes (and I know it could be made to do them). Another example: pt-query-digest’s tcpdump parser doesn’t pay attention to TCP sequence numbers, so sometimes it invents a really long-running query where there isn’t one.
(This blog post is an attempt to do a 37signals approach to prioritizing: the stuff people complain about repeatedly is what you should focus on. No promises about fixing the gripes—I just want to hear them!)