System Shock 2 was very linear. And there's nothing wrong with that; having a clear goal doesn't equate to unfun. Gabe Newell's Half-Lifes are notoriously on-a-rail (they even called one of the levels that!). Deus Ex was quite linear, too: there were distinct gates to the next level that could be achieved through a few different sub-goals, each of which could be, in turn, achieved according to the individual players' strategies (which I think is the best part of the game ... apart from the truth-in-plain-sight conspiracy, and the super-realistic science fiction and nanotechnology enabling magical abilities, and the super-duper graphics, and the sublime soundtrack, and the excellent writing, and the sensational gameplay, and the cynical social commentary, and ...).
The biggest improvement Bethesda made to Morrowind was, in my excellent and worthy opinion, the tracking system in the journal. (It was beyond tolerance to have to hunt through the hundreds of diary pages to find a quest that you wanted to continue in the local geographic zone.)