I'm not really doing to say anything about the RSE characters because I've never bothered to read that arc after I finished GSC. My least favorite characters as most people have already said are Yellow and Gold.
I don't hate Yellow, she's a cute character in her own respect. I just don't like how she's supposed to be the main character from Yellow version. She doesn't fit. She should be a side character if anything, but whatever.
I really don't like Gold. I was pretty apathetic to him in the games and once I got my Crystal version, I completely forgot about him and my Silver version. Both in the manga and the games, though, I saw him as a wanna-be Red. He dressed similarly to Red and looked up to him, but was in no way as awesome as him. I also don't care much for his cocky attitude, his gambling problem, and his over personality.
I suppose if anyone feels like hating me right now, they can go ahead and do so.