The most commonly accepted view on this subject is that Jenova is not a Cetra, and never was. This explains why Sephiroth isn't really a Cetra, although he thinks he is; and also ties in with Ifalna's story about what really happened when Jenova fell to the Planet. However, there are one or two theories that say Jenova could have been a Cetra to begin with - these are also discussed on this page. Please bear in mind that they are very unlikely to be true - it is basically a given that Jenova was not a Cetra at any point. Anyway, here goes...

1. Gast, Hojo and Sephiroth were wrong.
   Sephiroth believed that Jenova was an Ancient - Professors Gast and Hojo managed to make him believe that she was his mother, so it wouldn't have been hard for them to convince him that she was an Ancient as well. Having said that, at the time of Sephiroth's birth the two Professors were not aware that Jenova was not an Ancient - that was why the experiments continued to go ahead. It was only when Gast left the Project and Ifalna told him the truth about Jenova that it became clear she was not an Ancient.
   
   
   
   
   
2. Ifalna, a true Ancient, knew the truth.
   Ifalna, the woman whom Professor Gast fell in love with when he left the Jenova Project and moved to the Northern Crater, was an Ancient - she and Aeris were the last remaining true members of the Cetra race. It would be sensible to find the answer to our question from one of the Ancients themselves, and Ifalna provides exactly the answer we need. When she falls in love with Gast, she tells him that Jenova was an alien who fell to earth and tried to kill all the Cetra - hence their name for her, "crisis/calamity/disaster from the skies".
   
   
   
   
   
3. Jenova tried to wipe out the Cetra.
   Ifalna said that Jenova was an alien who tried to kill all the Cetra. If Jenova was truly an Ancient, why would she want to kill all the others? It is always made clear that the Cetra were a peaceful race, so the idea of an in-bred hater of the race hardly seems sensible.
   
   
   
   
   
4. Jenova wasn't human.
   As far as we know, the Cetra were normal humans and weren't able to fly. So, if the theory about Jenova falling to the Planet from the sky is to believed (remember her nickname, "crisis/calamity/disaster from the skies"), she can't have been an Ancient because - as we can see during the four Jenova battles - she certainly isn't human. It is, however, possible that she was human once and something caused her to mutate - perhaps exposure to the huge amounts of Mako energy in the Lifestream?
   
   
   
   
   

Note that these theories are very much speculative, and may not tie in with all the facts they should do.

1. Jenova was once a Cetra, just like all the others. Somehow or other she came to be infected by the virus (which others would have you believe she started in the first place) and it was contagious, so it was spread amongst all the Cetra. They went insane and turned into monsters, and most of them died. Jenova turned into some kind of super-monster and survived, only to be sealed away within the Planet by the few surviving Cetra. Basically Jenova was a Cetra who turned evil because of the virus, then went on to cause the whole Sephiroth problem when Gast and Hojo dug her out of the ground.
   
   
2. Whether or not she was a Cetra, Jenova certainly wasn't always the monster type thing we see in the game. Ifalna refers to the original form of Jenova (when it met/was the/a Cetra) as "him" - so it would seem that she has the ability to change her shape and appearance. (Then again, we already knew that. :P) Anyway - based on that evidence... maybe s/he was once a Cetra and gained the shapeshifting ability from the virus that killed the other Cetra?
   
   

I'd be interested to hear your opinions on this issue. If you'd like to comment, drop me a line and I'll add your opinion to this page.