If the naming of each series is that consistent, you could just use parameters in bash and build the new title out of it and then do the rename, in a loop. It would be a very short shell script.

eta: using printf to format the new title variable will let it handle the number formatting clearnly, like 01 for 1

eta: something like this

for f in *"Season "*; do s_ep="${f#*Season }"; s="${s_ep%% Episode*}"; ep_t="${s_ep#*Episode }"; ep="${ep_t%% - *}"; t="${ep_t#* - }"; printf -v new "S%02dE%02d - %s" "$s" "$ep" "$t"; mv "$f" "$new"; done 

mv “Star Trek Next Generation Season 1 Episode 1 - Encounter at Farpoint.mkv” “S01E01 - Encounter at Far Point.mkv”  

Or am I missing something about what you're trying to do?