Good point, and yeah, "it" meant metagross. A jolly metagross would really be a significant threat to Togekiss, but Flamethrower is playing it safe. Aura sphere is effective most of the time, but if you want to ensure a firey doom, flamethrower is pretty good.Err..."it" refers to Metagross, right? Metagross's max Adamant speed is 239 and the EV's I posted achieve 244 speed, so it won't outspeed you unless it's Jolly or Scarfed. CB Metagross would be a pretty significant threat, as MM does 81.92% - 96.61% to this Togekiss (probably enough to KO it considering LO recoil). Without a CB, though, it does 54.80% - 64.69%, so you can take one hit from it and 2HKO with Aura Sphere (and as I stated earlier, Flamethrower would really only be useful for Meta, Jirachi, and Bronzong. Zapdos will basically always outspeed you and can do a lot of damage with T-bolt, though it won't OHKO unless you've taken some previous damage. Nasty Plot'd Flamethrower won't even OHKO most of the time, so Zapdos is probably best avoided).
As I expect good counters for togekiss are the steel/psychic pokemon, so if you want to deal with them, run flamethrower, but for all-around coverage, I admit Aura Sphere is pretty powerful.
I forgot it until now, but my original point is that flamethrower should be an option on the set, as a possible replacement, which is up to the user to choose. Not like I'm trying to knock your set, Air-Fighting is generally more effective.