Err, no, any hacking of any pokemon is illegit. Even if you /had/ that pokemon and one time, it'd still be hacked, and thus you'd not be allowed to use it on wifi against people.
But, if you actually took the time to hatch and train the Pokemon legitimately to Lv. 100, and if you recorded its stats and other info for
backup purposes only, that should justify 'hacking' it in if you lose your save file or cart
on accident. If you have the original Pokemon, then you should use that Pkmn only, and only 'clone' it if it is
accidentally deleted. But if your file got deleted since you used AR for Max Stats or whatever, then you don't really have an excuse to backup Pkmn.
It would be really annoying if you had to waste time manually train the
exact same Pokemon
again with the Elite 4 just because of a game error (which Ash and co. don't even have to deal with!) The time you used up training the Pkmn you recaught could be used to train other Pkmn.
With Wi-Fi battling usage, etc., if you have a 'cloned' Pkmn because you lost your legit trained one, and the clone has the
exact same stats, IVs, nature, and ability as the lost legit one, that should justify the situation. With the method the Pkmn was obtained, the backup identical Pkmn
has been undeniably hacked into the game, but it is only meant to
rectify an accidental loss of data that can't be undone (technology simply has errors we sometimes can't control)
/replace the lost
legit Pkmn which was actually obtained through
legit means. So, backup Pkmn should be allowed in this case.