Me and my partner have had Lilly since she was a kitten she is now 2 1/2 years old - she is a very loving and good cat and loves the outdoors. she has never got on or liked other cats that are around, she will run and cower away from any cats she comes into contact with. about 2 months ago we decided to adopt sooty a stray cat who we think was treated badly at some point in her life. she is about 18 months old according to our vet. Lilly and sooty have never gotten on. everytime sooty comes near Lilly, Lilly gets very defensive and starts growling or hissing at sooty - this seems to encourage sooty to attack Lilly and a big scrap will start, it is a bad scrap as well fur flying everywhere - we have tried to leave them to sort their differences out but the fights get too bad that we have to intervene. we understand that they may never be 'best friends' but we want them to at least tolerate each other in the house. although sooty is a stray she has come round with me and my partner great she loves her new life with us and is now a very happy cat but we have to keep Lilly and sooty separated at all times because the fights are too bad. it seems like they are never going to get on or get used to each other as they cant be round each other at all! we love both cats so much and just want them to tolerate each other as much as they possibly can.
It sounds like Lilly wasn't socialised during the first seven weeks of her life. This is the time when cats should be introduced to as many other animals and people as possible, as this helps them become far more accepting of other animals in later life.
There are no easy answers to this one i'm afraid, you cannot force cats to get on and as you say sometimes they just don't.
I don't know how you first introduced them. there is a process which helps to introduce cats to each other so that they are more likely to tolerate each other. It may be worth taking a few steps backwards and trying that process now. It does take some time and effort on your part but if handled calmly and confidently can help.
I have written a page about this introduction process on my web site here
best wishes Kate