I know Fluther is nearly-perfect, but if you could, how would you change it?

There would only have to be a few tweaks. I would:
—Make it a little more like email. You would be able to see the whole “thread” of messages when you message somebody so you know exactly what you’re responding to.
—Make it a little more like Facebook. There would be “Fluther requests” like there’s friend requests on fb. Then you could see when people in your fluther are online, and there would be a notification of some kind when somebody in you fluther asks a question.