I've been thinking about this recently, especially in light of the discussions about what the original outline was versus what Joe had to do when Mike O'Hare had to leave the show. I have a cumulated many of the script books, but still have some holes, especially past the halfway point.
I think my biggie is Talia. I haven't seen this discussed in here, but it sure seems like they were setting her up to be the super-telepath to fight the Shadows, what with the fracture of her relationship with the Corps and Jason's tinkering in her brain (and apparently utterly missing the dormant spy personality). I like Pat Tallman, so I was quite happy with the return of Lyta and what had been done to her... but all the setup with Talia just getting flushed has always bugged me. I don't know what the original plan was for her. I know it's unlikely, but I love the idea of Lyta making her way back for other reasons and Our Heroes™ having *two* telepathic powerhouses on their side...