I have two guinea pigs, Delilah and Rose. Rose is a very mean guinea pig, I have had her for over a year with no progress. She is almost 2 now. Right from the start, I could sense she might have been abused. She absolutely hates being handled and constantly tried to fight Delilah (and did twice). I have been trying to work up a sense of trust with her, but it hasn't changed much at all. When I take her from her cage, I have to wear protective gloves because she will bite. I hand feed her sometimes and take her from the cage to bond. If she will even slightly cooperate, it doesn't last but a few minutes. I am not trying to make her friendly and loving like Delilah, but at least get her to trust me. I'm not sure what else to do. Hand feeding and bonding are all I can really find. I try not to bother her too much unless I am cleaning her cage. She is a little less mean once I get her out of her primary cage. While transitioning her to her travel cage, I calmly pet her and talk to her before placing her down, just to try and build trust. I respect her barriers and boundaries and don't want her to be uncomfortable, but it is really sad having two guinea pigs and only a bond with one. What else can I do?
As for the pigs themselves, as a positive: The pigs have a mutual respect for each other, and even when in separate cages (they have a large one with a divider as their primary) I keep them right near each other. They talk to each other often. I even see them cuddle through the bars sometimes, so thankfully they get along more now than in the beginning. I think they just like their own space.
Also, be absolutely sure there are no medical issues that could cause pain. A guinea pig in pain will lash out. Look at general health and skin issues (like mites) to rule out a medical cause.
One of the things that you have to do it to stop thinking of your pig as "mean." She's not mean. She's frightened and anxious. In truth, she's acting MORE LIKE A REGULAR GUINEA PIG than your friendly one is. Typically, if a guinea pig is given a lot of gentle handling right from the start as a baby, it will tend to be more friendly and relaxed around human's, but not always. I have had babies born in the rescue that have gotten tons of attention and handling and STILL act like your pig acts. Every domestic pig still has a bit of feral pig inside.
The problem is that, if you have it in your head that she's "mean," you will think that she's not a nice pig and you may come to resent her. She's not purposely being nasty to you and your other pig. What you need to do is to accept her as she is and try to find ways to make her more comfortable. If she doesn't like to be picked up, then don't make it your mission to teach her to like it. Accept that she doesn't like it (and probably never will) and find ways to enjoy her company while she is in her cage. Obviously, she will still need to be handled for nail trims, weekly weighing's and the like, but try to make it quick and as low stress as possible. Maybe she could be herded into a small carrier when you have to lift her out to clean the cage and that would be less stressful than chasing her with your hands and gripping her to lift her. Things like that.
And just in case, I will tell you about a pig that I fostered for the rescue. He was an older boar that was a big, friendly chubb-of-love...in his cage. But when he was picked up, he went nuts, fighting and biting. After a lengthy period of observing him (he never did "zoomies" in his roomy cage either) I figured out he was blind. Being picked up off his feet when he couldn't see what was happening scared the bejeebers out of him. He probably thought that he was about to be eaten.
It doesn't mean that, over the years, your scared one won't get more friendly, but it will take a long time and a lot of low-key, friendly interactions on your part to bring it about. Maybe someday, you will be able to get her to take food from your hand. Maybe someday she will let you scratch her under her chin. But if it doesn't happen, it's not necessarily a reflection on you. You still have the satisfaction that you gave her as good and as comfortable a life as you could. And you had a really great guinea pig as a pet.
I have accepted her as who is. I just feel uncomfortable, as she is, trying to handle her and having her freak out. I want her to feel comfortable with me if nobody else. She does take food from my hand, of course wanting to snatch it. I just hold it firmly and let her eat. I try only pick her up when necessary, no longer trying to sit with her since she clearly does not enjoy it. With Delilah, I can take her out and make my observations of her body myself. Check her fur, clipping her nails, looking for anything unusual, I can even check her teeth. The vet clinic has to do this for Rose.
My goal is to build trust or at least some mutual understanding that keeps us comfortable.