You know what? I went through this too, briefly. My first daughter was 5 when I got married and had my 2nd daughter. I noticed when the baby became a toddler, I was constantly annoyed with my older daughter. Her father and I split up under bad circumstances and she too looks exactly like him! He had a tendency to get himself in trouble, and when my daughter would act up, I saw that as a personality trait she got from him. I was able to put a stop to this for the most part. I love her and value the time I had alone with her raising her as my first child. It was so special, and my 2nd daughter will never know what it is like to experience that. So basically when I find myself really annoyed with her (she is eight now) I think back to how amazing it was to have my first little girl, with everything new and exciting.
Also, my 2nd daughter is very laid back and very different from her sister. I guess that is also a factor in how I treat them. My 8 year old seems glad to see her sister now getting into some trouble too! I know that I dont love one more than the other. I honestly cant see myself living without either of them.