Both Eden and Plymouth have their strong points. Thor's Hammer is hands down the most powerful weapon around.
Back in high school (and then one day a few months ago) a Friend and I used to play a lot of Op2 games together. He would always play as Eden, and I would switch between the two.
I won more with Eden, because of the sheer power - but I found that playing as Plymouth was a lot more fun! Ever smiled with glee as you stole all of your opponent's ConVecs and Cargo Trucks as you blast his Vehicle Factory to smitherines with a Supernova?
Playing Eden you have the same basic approach - overwhelm your enemy. Plymouth's lack of a killer weapon (such as the Thor's Hammer) forces you to experiment with ways to make up for that lack. Guerrila tactics and theft are much more fun than simply blowing up your enemy.
After I introduced my friend to the Thor's Hammer by levelling his entire colony with one small wave, he couldn't understand why I ever chose to play as Plymouth...until I turned around and cleaned his clock just as badly, with different tactics.
And besides, why build Thor's when you can just steal them and bolster your Plymoth Vehicle Fleet?