>>47217291It depends on what you're doing, I guess. You could make any villains be "stronger" or just more threatening than random trainers through various means. You could also edit the Pokemon in question. What Legendary Pokemon were you thinking of? One of the Sprites? A Dog? A Mew clone? The Regis?
If you're starting with the Regis you might want to give it to the player at level 40~50. Then give the Trainers you meet along the way similarly leveled monsters. The Regis are relatively easy to work around in this regard.
Also, you should limit the number of Poke Balls the player can access at the start of the game, or maybe even all of it, if it's just a short game. That way, even though their starter Pokemon is powerful, it will have its HP and PP widdled down over time by numerous fights. Space out healing zones appropriately.
It would be easier to help if we knew more about the story and which Pokemon you were thinking of using. Don't be shy.