In the Campaign mode I've always thought of Eden as the bad guys. After all, they were the ones who pushed ahead with terraforming and ruined relations between the colonies, not to mention creating/releasing the blight to begin with! I know it was a "accidnet" but why create something you're not sure you can control? Especially when you know that it could easily kill people!
Personally, I've always liked Eden. The Plymouthers were always a bit too... Hippy for me. Anyway, as two others have already pointed it, most in Eden had no idea the terraforming experiments were even going on. The "hot labs" were restricted to all but Nguyen and his crew. As was also said, Axen and others that DID know were against his project.
And you're all forgetting a side: What about the Eden Renegades? Though that could technically be the Plymouth storyline, I think they deserved more recognition than they managed to get.
Plymouths story was more gratifying, but I think Eden managed to atone in their own storyline by the end of the game, and even take down the "Masters", who were the "We're going to butcher all non-clones" people. The Masters were really the only people in Eden whom you could say were actually and truely "Evil".
And addressing more of the issue in Prometheus' post, Nguyen didn't even consider the possibilities of the Blight breaking down the bonds in a human body. You can say that he SHOULD'VE, but that doesn't change the fact that he didn't. They were certain they could control it.
You can also say that it was, indeed, Plymouth who destroyed inter-colonial relations by shutting down the only link between the two colonies: The Communications Satillite.
Besides, no one who's played the original Outpost can say that they didn't, at one time or another, mess around with Terraforming their planet.
