If you felt that 99% of the time there was only one path, you didn't give the game a chance, or you didn't bother to try to look for a different direction. You failed, not the game design.
The only time the game felt like it was on rails like that were the many (not all) of the fight scenes. You weren't supposed to fight, they gave you the tools if something got between you and your target you had a chance to eliminate it, but at it's core it was a runners game and you were supposed to run, not fight. And in most of those "guard" scenes of the game, there was a clear goal, but the way of getting there could have been through one set of stairs or jumping down from a high ledge or using scaffolding to get up and around. The environment allowed for a free reign of options even if you were stuck in a box corridor with the goal at the other end.