I have a few ideas.
First and foremost I think the internet needs to focus on one issue at a time. Once you divide the activists the whole message gets blurred and no one cares. (Case in point, look at occupy wall street, what exactly did the protesters want??)
Point two, it can't involve petitions, those are stupid and counter-productive.
Point Three, activists like to be involved. Have a way for people to earn points contacting their representatives or helping the site in other ways and perhaps be able to use those points to vote on what issue to tackle next, or the actions presented for an issue?
Really I'm picturing something like a cross between reddit and stack overflow geared towards political action. Power users can vote on issues, have meta discussions in the background, but normal users just see the one issue that's going on at the moment with a simple interface that explains the issue and has 1-3 meaningful actions they can take.
My thoughts for the 3 actions could be: Call your representative, Request a pre-addressed envelope be mailed to you so you can write a letter in your own words, or donate money to pay for mailing the pre-addressed letters to people.