I know there have been episodes where the intention was to have certain characters in them, but, due to scheduling, they weren't available. For instance, Billy gave some lame ass reason for not going with Laura when she broke out of the brig and escaped off Galactica because Paul Campbell had to shoot a pilot and they had to write him out of the next couple of eps. Rick Worthy's work on Eyes may have been an issue during his early appearances on BSG, but in Seasons 3 and 4 Simon could have and should have had a bigger presence.