Is it wrong to use legendary Pokemon?

Answer 1

Definitely not. If the Pokemon is available, you can use it. Though, to a certain extent, the use of legendary Pokemon can be wrong.

If you have an entire party of legendary Pokemon, then it is wrong, since legendary Pokemon are much stronger than any normal Pokemon you could find more than once in the wild or any starter Pokemon.

Keeping only one or two legendary Pokemon keeps the game fair. Think of it this way - if you were to battle a friend, would it be an unfair battle because he/she doesn't have that legendary Pokemon?

Exceptions to the use of legendary Pokemon include the in-game legendary Pokemon, such as Lugia and Ho-oh in Pokemon HeartGold and SoulSilver (along with their respective Hoenn legendary Pokemon). Since these legendary Pokemon come standard, there isn't a reason not to use them.

Pokemon such as Deoxys shouldn't be used, since Deoxys is more than extremely powerful and poses an unfair match for any other Pokemon, including some legendary Pokemon.

In short, it is wise to keep only one legendary Pokemon that isn't from an event in battling others, but for the purpose of defeating the game, go ahead and use the legendary Pokemon. If Nintendo didn't want you to have such a powerful Pokemon, they wouldn't have created it.