What could have worked in the 'convince Eden is wrong' idea would be prior quests or discoveries of notes, tapes etc. where prior 'good' ideas of Eden and the Enclave were shown to have a bad effect on the very world that Eden thinks it is helping, something along the lines of telling the Master that mutants were sterile AFTER finding this information out from somewhere else before.
Why not in your travels run into Enclave defectors, victims etc. who have information about prior Enclave schemes hatched by Eden and then depending on how many things and how detailed your accumulation of knowledge is, you can confront Eden with as many failures as possible. If you only have disjointed info you fail to convince Eden, but you may be able to bluff him with a very high speech skill as well. If your data is thorough, then Eden will give up regardless of speech ability.
I don't know, some shit like this is hardly groundbreaking, but I came up with it in a minute, and it would hardly have been difficult to implement.