After the last donor call where they called and asked me what I wanted them to focus on, I said "end the war on drugs." I was told that was not in the mission statement. the kid on the other end of the phone call was polite, but I felt like I was being taken advantage of for a paycheck and they did not really give a fat flying fuck about what I want out of the organization.
I do not know how the ACLU operates, but I'm giving them the benefit of the doubt here. In their defense, even their resources are limited and the war on drugs is a contoversial issue. They probably want to have as much impact as possible, so supporting things like the rights of women, gays, and minorities (Lord, I can't believe this is still an issue), ammendment issues, due process, etc. are probably the direction they want to go in because that's where they believe they can do the most good.
Specialized organizations like the EFF are specialized for a reason. So for those of us who have issues of particular concern, they can be very good resources, provided they're on the up and up.