Put simply, for the single player campaign. Would you prefer an: 'Eden and Plymouth campaign' or a 'New Haven and Plymouth campaign'?
I won't do three as that would require 3 tech trees, three campaigns, 3 stories, 3 unit and vehicle types....etc.
As for a simple overview of each colony's strengths:
Plymouth, same as op2. Better at civil and use projectiles and explosives.
New Haven/Eden, same as op2. Better at tech/research and use energy weps.
I was going to have some new morale structures for eden anyway to balance the game against plymouth. (it's not fair if plymouth can raise their morale much faster and grow quicker than eden in multi).
Because of what happens at the end of op2, where the remaining colonies join to escape new terra and go after plymouth. They join together so I feel New Haven makes more sense. But many people might like the classic name of Eden.
But the bottom line is it's just the name:
Eden or New Haven?