I actually didn't enjoy this game, which surprised me because I was such a Ratchet fan. The Clank sections were fun, but the Ratchet sections seemed so uninspired and generic. Even the graphics in some areas seemed to lack the polish of past games (One forest area in particular springs to mind). And the space area was a huge let down.
As for the story... The new character they added was flat out awful. Annoying and unlikable. What happened to the girl from the first two? They just dropped her. I hate when characters get dropped for no reason. Rather than making it a really cohesive trilogy, they sort of just went as they go, which made the story seem very mish-mashy.
I never actually finished the game, though I came close. I got to a point where I needed to go and collect more Zoni, and just shrugged, said "Fuck you Insomniac" and put the game down. Had this been a year ago, this post would have been four times as long, probably with more swearing. But alas, I was not a member then, and now my memory has faded. I should go back and play it again. It has a good rep on GAF. I wish I could understand why.