Mmm, well the idea of Legendary Pokemon is largely a gamble. Of course it would be unwise to add them to the "catchable" list, considering there are people who would invest way to much time into just filling their team with all Legendary Pokemon. Which would ultimately make game-play much harder and in some cases, less fun, for new players. Not to mention the whole mess if guilds and parties like Team Rocket could be formed, which of course, would be able to attack anyone on a whim. Then for sure we would have some people who love pvp, go and kill new players for "their" amusement.
However, the idea of adding them as a STORYLINE character, or boss type Pokemon would be a fun idea.
(: