The problem wasn't necessarily in its linearity... it was the fact that the linearity felt forced and artificial. For instance, it drove me crazy the business with the boats, and the idea that a flimsy wooden wall was all that was keeping me from leaving an island. Why couldn't I just climb over it, burn it down, or swim around it? And for that matter, why would you need more than one boat to travel from island to island? Wouldn't the one you got on the first one suffice?
In my opinion, the most worthwhile thing from GF3 was Khyryk. I only actually played through it once. I was playing as a canister-mad rebel, and the extremist attitudes of most of the Shapers I'd met didn't convince me much to join them. Then I ran into Khyryk. Perhaps a bit late in the game to change sides, but Khyryk was enough to convince me to join the Shapers. I even went back and killed the rebels on the second island and destroyed the Creator on the third... even though the ending dialogs didn't acknowledge some of the stuff I'd done. But in the end I found that much more satisfying than having been a hardliner for either side.