What is the origin of the minhag of kapparot? What if one chooses not to do the minhag? Is one less favoured by God? Is there a certain benefit to doing kapparot?
The origin is unknown outside of when it is first mentioned. The earliest mention of the practice comes from Rav Sheshna Gaon who lived in 660 C.E.
One of the reasons given for why a chicken is used is that the Hebrew and Aramaic words for one another mirror each other.
The Aramaic for Chicken is Gever. The Hebrew for man is Gever. The idea is you're taking a chicken to atone for a man and so it's a symbolic play in language.
You aren't required to use a chicken for the practice. While many Jews still continue to use chickens for the practice, there are those who instead use money to gain the same spiritual benefit.
There is actually a long back and forth in Jewish history regarding the practice. While many Jews consider it acceptable and continue to do it, there has been a suggestion it's problematic because the practice is very similar to non-Jewish Amorite practices which existed historically. For this reason many notable voices in Jewish history rejected the practice and argued against its continued use.
Rabbi Yosef Karo was one of the more famous examples of a respected Rabbi who rejected the practice. While many of his opinions and positions are endorsed by many in modern Judaism but his opinion on this practice wasn't one of them. Hence it has remained an active part of sin ritual in Judaism.
The origin is based on a pun: גבר can mean both 'man' and 'rooster', so the Geonim (the Amram Ga'on I think) concluded that a rooster could stand in for a human being when it came to repentance. It's not a commandment so there's no obligation to do it, and God is unlikely to mind.
Benefit... that's about what's spiritually fulfilling to you. I suspect the animal rights lobby would criticise those who choose to do it, however.