For me, Cyclonus was always a rebuilt Skywarp, as it just made the most sense. Skywarp was a jet with purple highlights, Cyclonus was a purple jet. Plus, it would make the most sense to assume that Skywap and Thundercracker, two prominent flying Decepticons would become Cyclonus and Scourge, two prominent flying Decepticons. The Insecticons became Scourge's Sweeps.
I tend to believe Cyclonus' "Armada" never existed, and thus has no pre-Battle of Autobot City counterpart(s). Why?
It's pretty much been confirmed that the inclusion of the line "....and his Armada" was a holdover from a previous version of the script where Cyclonus, like Scourge, would have his own army of identical warriors. That idea was dropped, and only Scourge's Sweeps made the final cut, with Cyclonus' Armada being written out. This is supported by the fact that no other warrior or warriors resembling Cyclonus are ever seen.
Now a lot of people will say "but that doesn't matter, the line '....and his Armada' as well as an other Cyclonus are shown. Therefore at least one other Cyclonus-like 'Con exists officially."
To that I say you can't take production and animation errors as cannon.
Yes, the line"....and his Armada" is spoken. But that was just a holdover from an earlier version of the script, probably left in due to an oversight, and was not meant to be included in the final product.
Yes, there is a second Cyclonus-like 'Con shown, but in addition to the above mentioned reason of being a holdover, it can also be described as an animation error, something the G1 show, and even the movie, had in spades.
Simply put, you can't take everything you saw animated on the G1 show as cannon.
So to me if you're going to accept the existence of Cyclonus' "Armada" as cannon because of animation and production errors, despite the fact that the Armada is never seen afterwards, then you also have to accept that after the Battle of Autobot City a still-functioning Brawn switched sides and became a Decepticon.

So if we accept the fact that there's only one Cyclonus, and no Armada, then who gets to be Cyclonus? Skywarp or Bombshell? I say Skywarp because.....
Like Cyclonus he's a jet with purple colouring.
Like Cyclonus he's a prominent flying Decepticon.
Like Cyclonus he's loyal to Megatron/Galvatron, while Bombshell, being an Insecticon, was much less loyal to the Decepticon leader. So it would make sense that a loyal soldier of Megatron's would be rebuilt into a loyal soldier of Galvatron's, while someone like Bombshell and the rest of the Insecticons, who were much less loyal, would be demoted to minion status.
So for all the above reasons I tend to think that the rebuilding of the discarded Decepticons goes as follows....
Megatron becomes Galvatron.
Skywarp becomes Cyclonus.
Thundercracker becomes Scourge.
The Insecticons and any of their clones that were discarded become Scourge's Sweeps.
The continued appearance of Insecticons after these events can either be described as animation errors or the more cannon-friendly explanation of being one of the many Insecticon clones that wasn't discarded.

QUOTE (Now Look! That Alien Guy! @ Nov 17 2007, 11:56 AM)

better question: why does Galvatron get to keep his memory, but scourge and cyclonus don't?
How do we know that? Neither Scourge nor Cyclonus ever say "I/we have no memory of who I/we am/are prior to Unicron creating me/us."
For all we know they retain the memories of their previous incarnations.
If you want a cannon-friendly answer, however, I have that as well.
Megatron's memories were to important and vital to be discarded, so Unicron felt it necessary for Galvatron to keep the memories from his past life. Unicron, however, didn't feel that Thundercracker and Skywarp's memories were vital, so he erased them from the minds of their new forms Scourge and Cyclonus.