So? There have always been massive uber-weapons in a lot of sci-fi. All that really mattered to me was the storytelling. If you focus on that you are missing all the other elements that made the Xindi storyline mostly successful in my opinion.
The arc was definitely plot-driven with some character work for Archer and T'Pol and of course there was plenty of action but the stories didn't exist solely for action but rather action was an expected element of the situation the crew found themselves in. It was no more out of place or in danger of overshadowing the episodes than the action quotient we were treated to in DS9 during the War.
How can you say it was not plot-driven with the weapon, the race to stop it, looking for the Xindi, the spheres etc.
As for some of the character work we had Archer being faced with some hard decisions leaving behind his easy-going persona from the first two seasons. Then T'Pol's arc of self-discovery and struggles with emotions that had been touched on a lot in the first two seasons finally take a dramatic turn when she becomes an addict and all the consequences that followed.
I thought it was a pretty neat idea that we hadn't really seen before in Trek. As for how plausible it might be scientifically I could care less. Trek is fiction and I'm willing to allow the writers some latitude in order to tell an interesting story.
