First, my distaste for the Green Party's methods in campaigning. As reported by CBS News, they accepted money and assistance in 2006 from then-senator Rick Santorum of the Republican Party in order to get on the ballot. The state's high court threw candidate Carl Romanelli off the ballot citing insufficient signatures, but the story exposed an even deeper rot within the Greens' political machine in Pennsylvania: the willingness to be compromised just to try to stick it to the Democrats, whom Greens consider little or no better than the GOP.
There is, of course, a valid argument to be made in claiming there is difference between the two major political parties. One need only look at the voting records of the two Prima Donna Democrats competing for their party's nomination to run for president, and the complicit cowardice by most Congressional members in either chamber, to see the truth in this point of view. But for the Greens to accept help from a GOPer so vile as to have had post-anal sex discharge named after him reveals both a lack of integrity and a sickening display of hypocrisy. Such actions add otherwise undeserved legitimacy to charges by Democrats that greens are somehow bent on "stealing" votes they feel belong to their party.
Then there is the organization of their campaigns for national office. Or, rather, the lack of organization. As I have pointed out in my recent three-part series on Progressives, Liberals, Movements and Political Parties, trying to run presidential candidates before having secured enough state-level offices (especially state secretary, judicial, and legislative positions) waste resources that are better spent building up presences in the various states so as to achieve the ability to gain traction at the national level. What good does it do to run candidates for president when the Green Party hasn't even made headway winning state legislative and executive offices first?
That's why I think it's better to rally the Progressive Movement through its own namesake political party. I'm not saying we can't or shouldn't work with Greens; since their platform so closely matches that of the overall Progressive Movement, they make natural political allies and might even be tempted to switch over. But I think as long as some elements in the party are willing to help Republicans, and as long as the party leadership insists on trying to build the party in a more top-down manner, their effectiveness as a political party is severely limited.