I always took Jenova's shape as a female to just be reflective of the last human/cetra form infected by "the virus".
With Jenova being tied to The Thing in terms of how it was conceived, I always imagned Jenova was basically just a bunch of cells in the first place - like a virus - whose property is to infect other organisms. The whole shape-shifting/mind-reading thing is just a automatic mechanism that activates as a self-defense/propagation tool once the virus has sufficiently altered its host.
I imagine the first meteor striking, and some poor Cetra sod heading over to investigate, only to get into contact with the virus, and then begin to mutate.
The thing then heads back into town and starts killing/infecting others.
Jenova as we see her in the game, is just the last remaining cell-cluster/infected Cetra.
The reason this form is retained when you fight Jenova, is because whatever else it is, its still the primary cell-cluster.
Sure, Sephiroth can command it to change shapes, which he does, but ultimately, once he/it releases the guise, it still reverts to its original form, the last thing it infected and whatever appearance resulted from the mutation at that time - which just happens to have been a Cetra woman.
I think it's important for Jenova to not take center-stage as a villain in "her own right", because it conflicts with the larger theme of FFVII as a story.
FFVII is man VS nature, technnology VS naturalism.
This is the core theme that the entire game shapes itself around.
Introducing Jenova as a separate villain detracts from that, and takes what is otherwise a very grounded story thematically(keyword, I'm not saying FFVII's story is grounded in general), and makes it unrelatable to any real world topic or issue, which is completely uncharacteristic of FFVII in almost every other regard (hence why I don't think Jenova being in control, or even being a central agent are particularly good theories).
Getting specific though, sure, Sephiroth's psyche is damaged in a sense by having been born under the influence of the Jenova virus, but the entire point of the final scene in the game, where Cloud confronts Sephiroth within the lifestream post the destruction of Jenova is, I think, meant to symbolize the existence of mankind's darkness as an inherent part of Sephiroth as a person whether he'd been injected with Jenova or not - which is consistent with the theme of the game.
EDIT :
I think it's important to remember that Sephiroth's statement that he thought he was special, in many ways echoes/mirrors the ego displayed by his father Hojo, a person who is not infected with Jenova cells (but then actually injects himself with them). Sephiroth is, I think, probably meant to be a flawed character, Jenova cells or not.
Mankind is the planet's biggest potential enemy (hence the ending with the ambiguity surrounding whether holy wiped out mankind etc) and all people have some character faults in them (this is apparent in main cast itself as well). The more you shift the plot towards Jenova as a separate and influential entity, the more this is lost in favor of a completely abstract and unrelatable man/planet VS Alien conflict.
Not only is it a worse theme for that reason, it's a theme that isn't consistent with the rest of FFVII's story-telling as a whole, with its heavy focus on situations running analogous to real world socio-political issues that were on the forefront of discourse in the 90's (ex. natural gass discussion raging at the time) and other more personal issues like identity and character flaws like conceit and inferiority complexes.
EDIT :
Having structured my thoughts around it some more, I think I'd argue that Jenova serves no thematic purpose, and that trying to make it/her serve one inevitably leads to a bumping of heads with the other primary theme.
The purpose of Jenova is purely instrumental, or utilitarian. She is the catalyst for the plot, not a thematic set-piece.
You need a Jenova in FFVII to make anything happen, unless you just want it to be a plot about fighting a greedy global corporation.
Jenova is an instrument for the purpose of demonstrating the unscrupulous nature of man - where, when discovered, she/it becomes a tool for the Shinra military-industrial complex which is what generates Sephiroth, Cloud, and their entire conflict. She/it is basically the puzzle-piece that ties all the plot elements together and gives a natural-feeling reason for why things unfold the way they do.
If you suppose Jenova is symbolic of something, this just begs the questions, what, and for what purpose?
What room, or use, is there for an iteration on the biblical scheming woman-figure in this story? And what sense does that "analogy" even make when Jenova isn't even human in the first place?
Human women are bad because alien is bad? Alien is bad because human women are bad? Just, alien is bad? Do we even think that's a message the writer of FFVII would want to propagate?
How does this fit in with the rest of FFVII's narrative? What purpose would that symbolism serve?
Non at all in my opinion.
As I already said though - why would you make a symbol for alien dangers/evil/corruption in a story so deeply rooted in, and intent on showing the concept of danger/evil/corruption coming from within humans themselves?
I don't buy it. Jenova is just a catalyst - A plot convencience for the sake of putting everything else into motion in a justifiable manner. And, that's all she can ever be as far as I'm concerned without taking away from the theme of the game.
EDIT 2: (lol so many edits)
Totally as an aside, and almost certainly me reading way too much into the writing of the game - I've always liked to think of the 4 ending fights as being a condensed symbolic run-down of the basis arch of the game as it pertains to Cloud and Sephiroth's relationship.
1. You fight Jenova first - because she's the catalyst for everything that happened. This is the beginning.
2. You fight Bizarro Sephiroth, which symbolizes pre-nibelheim/Nibelheim Sephiroth. His monstrous form runs analogous to Sephiroth's own characterization of himself as a monster during the incident, and the small Jenova shape on his head symbolizes how the Jenova cells has tampered with his psyche.
3. You fight Safer Sephiroth, which symbolizes post-Nibelheim Sephiroth after he's travelled through the lifestream and attained the knowledge of the ancients. This is Sephiroth having transcended the Jenova cell's influence.
4. You fight the real Sephiroth, which is the core of his persona - a symbol of his ego, and the worst aspect of humans. He smirks at Cloud as he descends to him because, deep down, this is what he really cares about.
Sephiroth's ego is what drives him, a feeling of being special and better than everyone else, which Cloud denied and broke when Cloud overcame him in a match of brute strength within the reactor despite by all reasonable accounts should not have been able to do so (something Sephiroth expressed complete incredulity over).
This is why, despite having stated his goal is to become a god and travel the cosmos, everthing Sephiroth does throughout the game results in leading Cloud on back to him despite how it plays out through entirely unnecessary contrivances.
This also compliments the consistent thread throughout FFVII about unreliable narrators.
Everyone in FFVII are unrealiable narrators - even Sephiroth.
In the end we see Sephiroth's pure ego facing off against Cloud, the person who irrepairably bruised it - making the encounter a symbol for the better nature of man (Cloud representing compassion and care for his fellow man/planet) and Sephiroth being a symbol for man's worse aspects (Narcissism, delusions of grandeur, lack of empathy, solipsistic thinking).
