Nader declined. He specifically stated he did not want a Green Party nomination.
Nominating no one would truly be marginalizing the party. Instead they got an experienced and well known politician with strong convictions who aligns with the platform pretty neatly. I think any politician with strong opinions is going to end up being bashed pretty hard in the media. It is the nature of the game.
Is the Green Party pushing itself to the irrelevant and anonymous spectator sidelines or carving out a solid niche along the sidelines? (The system is way to rigged for any third party to be anywhere else.)