I think that's an interesting idea, but as soon as you decide on a platform -- even a really basic one that aims for inclusion/agreement among many non Democrat/Republican groups -- you begin to exclude. It's a really tricky issue to tiptoe around. I think it probably boils down to conflicts on two axes: priorities and "dealbreakers." For example, progressives and Ron Paul supporters agree on a lot in the abstract, but have very different priorities. Things that Ron Paul supporters care strongly about (audit the Fed, for example) are also-rans on many Progressive lists of demands. Similarly, you have "dealbreakers" -- a great example is taxation. The Green Party and the Libertarian Party also agree on many, many issues, but as soon as "regressive [flat] taxation" is bandied about, Green Party supporters are out.
It's a hell of a task to create a platform that 1) focuses on the similarities between these groups 2) doesn't prioritize one group's goals over another and 3) doesn't lose support out of either having prioritized the wrong things or tread too far into "no way can I support a party that does [x]" territory.
What if the purpose of the party were just to tear down some of the institutional barriers to third parties as a whole? This should make it amenable to supporters of those parties, whose supporters are surely fed up with these barriers and recognize the need to address them before they can make real inroads into America's electoral landscape.
The Protest Party Primary could just involve "candidates" arguing for the best simple "demand" to make, one that would be likely to give the other Third Parties more power in the future while also being somewhat acceptable to a Major Party (so as to be feasible). One possible demand would be "Institute the Alternative Vote." Voting methods are currently a state issue, but it could be made a Federal power through an amendment.
No need to bring up the Fed or Taxation. Indeed, the whole problem is that We The People have no voice on such matters due to all the corruption. The Protest Party would be about overcoming the corruption (thereby making the Party itself obsolete). I don't foresee any Protest Party candidates actually being elected. The idea is to get enough support (maybe 10% in Ohio, where I now live) that one of the two parties accedes to the Protest Party's demand. The Protest Party would then throw their support behind that party for one election.
This is what Ralph Nader was hoping would happen with the Al Gore and the Democrats. He often says all they had to do was take on the Green Party's platform. The problem, of course, was that the Green Party's platform was complicated and divisive. The Protest Party is designed to be simple and agreeable. Also, unlike the Green Party, the Protest Party would make explicit their demand and their intention to back the acceding Major Party.
I know it seems convoluted. It probably won't work, but I haven't seen any better ideas. To paraphrase Larry Lessig, when the alternative is giving up on America, what choice do we have?