(This is G1) I have no idea where this came from- it just did. Anyways, in Cybertron, ever since after the Quintessons were overthrown, It has sucked to be a femme. Their treated like second class citizens, or even worse, like objects by the mechs.
The difference between Mechs and femmes is that femmes have larger, and slightly different sparks then mechs. These different sparks allow them to have a higher chance of successfully and safely creating and carrying a sparkling- mechs can too,its just way more common for a femme to because of how unsafe it is for a mech to carry a sparkling (The spark, not the actual body frame). Most sparklings either came from Vector Sigma or Femmes. Anyway, because of their different sparks and programming, femmes have to use the slightly less durable femme body frames to accommodate for their larger sparks in their chest area.
At some point during or after the quints left, femmes were targeted because of their weaker, less durable body types and labeled as wastes on society. After a while the femme population was oppressed- it's almost impossible to get a job if you are a femme, and most are forced to do things that they would rather not, or join the steadily growing underworld. Anyway, its gotten to the point where even the history of Solus Prime, the first female Autobot (and, subsequently only female Prime) has been erased. (I know that that is TF:P cannon, but... Eh, AU?)
From the shadows, before the Autobot-Decepticon War a steadily growing group of femmes gather under the banner of Solus Prime, because she did exist. Meanwhile, some femmes hide in plain site as mechs, living as normally as possible while hiding their secret. These femmes are able to use mech body frames because they were forced into them when they were sparklings, allowing their sparks to adapt.
Anyway I thought about the stories of some of these femmes- and theoretically this would all take place during cannon, just slightly different- (like the original 13 primes thing)
Ariel/Elita-1:
Ariel was sparked in the slums of Crystal City, and made a living for herself doing... less than savory things on the side in order to make ends meet for herself during her younglinghood. During the early years after reaching adulthood (like 18-20) she fought in cage fights, before she gained enough credits to move to the Iacon Docks- where they don't care what you are, only that your productive. Making close friends with fellow dockworkers Orion Pax and Dion, Ariel enjoyed what she currently had. However, she could not stand for the suppression of her and the rest of the femmes, and with joined the shadowy group known as Solus's Femmes (Or whatever you want), and made many allies that would join her and her group of female Autobots after she was reformatted into Elita-1.
Other Female Autobots
Most of the female Autobots known through cannon came into contact with Elita-1 through Solus's femmes, and that is how they joined the Autobots rather then joining the Decepticons- Elita/Ariel was well liked and respected, and learning that she had been shot by the leader of the decepticons was not the best way to endear himself the the femme population.
Starscream
Starscream was a genius- that much was plain from the minute she was created. However, she was not in a very good position to show it. Being a flyer was already horrible- the council had never had a very high opinion of seekers, and life was difficult for anyone with that frame type, most of them being forced to stay in the city state of Vos. It was even worse for the Seeker femmes- while seekers themselves were less likely to care about gender, the rules and regulations imposed on them by the council made life a living pit for the seeker femmes. When Starscream was the human equivalent of 16, she went through a lot of slag to procure the one thing she wanted- a mech frame. She shouldn't have survived the transfer, but managed it (we all know that Screamers spark wasn't normal). Anyway, through a sequence of events involving blackmail, murder, and a lot of difficult to procure credits later, and the mech Starscream arrives at the Iacon Academy of Science. After that, she meets Skyfire, and we all know what happens from there.
... And then, during the course of the war, she discovers two seeker femmes in similar circumstances to her, and they form a trine, because why not?!
Mirage
Let's just say it was horrible being a femme in the towers, and that Mirage got moved into a mech frame as soon as she was sparked by a disappointed (and embarrassed) father/mech creator/whatever their called. It might actually be worse for tower femmes than it was for the femmes living in the slums. Make of that what you will. Mirages younglinghood was... not happy. Poor mirage.
Also, just because I can- Sunstreaker and Sideswipe, and well as Red alert. Because Why not? Ratchet is the only Autobot besides maybe Prowl who knows that some of the mechs are not mechs.