JMS chose Brother Theo's level of involvement.
Starting in early Season 4 most of the station limped along in complete depression. Ivanova had all the viewers with shotguns in our mouths as she suffered through the hour of the wolf. I believe it would be neither out of place nor out of character for Brother Theo to attempt to raise morale around the station. On the other hand, there were a lot more plot lines in motion at the time, and they were probably more important.
Furthermore, Lyta entering Ivanova's quarters with a bold, desperate plan to find Sheridan is certainly more exciting than the rudimentary, realistic scene of Brother Theo telling Ivanova about the power of hope. (Now that I think about it, the two different scenes would work well if blended; Brother Theo gives his inspiring spiel about faith managing. Ivanova voices her disbelief, but just as she finishes her link signals, and it's Lyta with her plan.)
Shortly thereafter, Sheridan returns "from the dead." This kind of setup - a member of the clergy and a "resurrected man" - has not occurred since . . . Peter and Jesus. The rumors of Sheridan's return would have Brother Theo undeniably be curious, and that curiosity would lead him to Sheridan's doorstep.
Now suppose if Brother Theo managed to catch Sheridan with Lorien there. The discussion among the three of them would probably have little to do with the Great War, but it could have been one of the finest exchanges of the Series. Imagine.
An appearance would have been possible in "The Illusion of Truth" with Dan Randall portraying Brother Theo has the stereotypical religious fanatic, despite the kind, honest words he would have about Babylon 5. Hmm . . . maybe it is a good he didn't show up in this episode.
After this point on the Babylon 5 timeline, the fast, furious road to Earth begins. An appearance could have been made in any of the episodes in the second half of the 4th season, but that doesn't mean an appearance is warranted.
With the start of Season 5, JMS does not have an excuse for utilizing Brother Theo. The idea of a Brother Theo episode sounds phenomenal, especially at the beginning of the Season when he could have been used so effectively. The title "Secrets of the Soul" unfortunately belongs to a lame episode about the Hyach, but it could have been a stellar outing concerning our man Theo. Any viewer that trades an outing like, say, "Learning Curve" for the potential success an episode about Brother Theo brings is joking--no argument.
It's possible that Louis Turenne's health played a part in his lack of exposure, but the three strong appearances he made in Season 3 cemented the character of Brother Theo as a part of the family. As I said, JMS chose the character's level of involvement, and JMS chose wrong. It is one of the greatest shames of the series that we have to ask whatever happened to Brother Theo.