Blah, blah, blah - Ony deep breaths more - blah blah...woah what?
Onyxia? Again? What a friggin lore whole this is. Even with the CoT instance, fighting Onyxia brings up some serious issues with the game, but they are ones we can work around.
Problem 1) In offical Canon Lore - Varian kicks Onyxia's tail all over Azeroth and his doppleganger self dies in the process. Onyxia is dead. Long live the King.
Problem 2) I've personally hung her head on the walls of SW no less than a dozen times. Someone get me a torch, we're stopping this regeneration.
Problem 3) Onyxia was a major hurdle. While this is coming in November, that tells us that IC isn't coming until Christmas (always nice when you can deduce timelines). Even if the fight is trivial, this is 3.2.2 and has been touted as a 'content' patch. Interesting.
OK - so how do we fix this?
The easiest solution is COT. Maybe we go back and fight in some kind of encounter that would prevent the time guys from borking her capturing of Varian. Seems kind of like a cop out - and if we kick her butt, how would that help?
Second, and my favorite, gets really convoluted.
Deathwing (Neltharion) is still alive and kicking under Grim Batol. He's been locked behind the doors, guarded by the Red Dragonflight, and who knows what he's been up to. Ideally, I'd like to think he's busting out X-man style, and maybe has made a deal with Arthas in the interim.
He's had some setbacks in the death of Onyxia and Nefarion, plus his Twilight Dragonflight has gotten pushed over with the deth of Sartharion and his brood. Deathwing has to be getting desperate at this point, even though he has been planning to take over the world since before the sundering.
So maybe he makes a deal with Arthas to raise his brood as skeletal dragons, offering to help topple the opposing army, and swelling his undead army with fresh supplicants. Fighting Onyxia as some kind of undead would be a neat twist - and fighting Deathwing (because you know Arthas wouldn't make a 'real' deal with him).
All of this is even cooler with some of the datamined information leaked about Cataclysm. We may actually be fighting Deathwing in the next expansion - after we weaken him in IC that is.
Or they could just add Ony without any lore as another way to help get loot to non hard mode raiders.