OK, I did finally have one problem, albeit a minor one. I came across a location where you have to defeat all the enemies in the area before a platform will appear to take you to the next section. After defeating all the enemies, the platform never came. Of course, I didn't know at first that there would be a platform appearing so I spent a good 15 minutes at a complete loss as to what to do next. I decided to just jump off an edge and die so I could restart that section. That's when I realized, during the second playthrough, what was really supposed to happen...
Now that I'm done with the game, I do have to agree with you, Repairman Jack, in saying that the story and level design were sorely lacking. The game is still pretty fun to play if only because it has the first two games as a foundation for its gameplay, but the series definitely didn't go out on top. That major plot development near the end was a real stinker...