Screwed by the Network: Not to a Fox level, but the Sci-Fi channel's commercials - and airing of episodes wildly out of order, showing all the raunchy ones back to back though they did show them in order eventually - would lead you to believe that it's porn dressed up as Space Opera.
To be fair to the network, they did give us the fourth season out of fan demand when word got out it wasn't going to happen, which is more than they did for Farscape. Also, when the September 11th attacks happened during the middle of season four and a new episode was preempted for a network-spanning broadcast about it, many fans found the tribute show ultimately depressing instead of uplifting and stayed up in the hopes that the late-night encore would be the new episode; it wasn't, but instead of just re-running the previous week's show, they had the thought to re-run fan-favorite Brigadoom.
What Could Have Been: Eva Habermann could've been Zev for the entire run; she left because news about season two was taking so long that she had to choose between taking other work or banking on the show getting picked up.
On a smaller scale, the original plan for Lyekka Vs Japan was to have Wist from Eating Pattern come back, but the actress was unavailable.