Substitute is recommended on many of Smogon's sets for Sceptile, and the reasoning is generally the same across the board: it gives Sceptile more breathing room to force progress without worrying about priority or status.
Sceptile's potent combination of high Speed, Substitute, and Leech Seed gives it a fair niche in earlier Generations (III and IV), while the presence of Sceptilite in Generations VI and VII makes Substitute more common on offensive sets as well. Both variations, SubSeed and offense, are effective in Generation V's lower tiers (obviously sans Sceptilite).
Sceptile doesn't really run Substitute in Generations VIII and IX, with it tending towards 4 attack sets or 3 attacks and 1 boosting move instead. The move is similarly unheard of in doubles formats, where Sceptile is almost always ineffectual even when run optimally.
Sceptile (Smogon)