There is none. The only reason is as a compromise to get the gay-haters to shut the **** up about it. Except, you don't compromise on human rights unless there's no other way at all. Civil unions would be a step in the right direction, and if it's the best that can be done now, then go for it. And don't stop pushing for the real deal.
Marriage should be open to everyone. Civil unions should be even more expansive. Civil unions are for your two old aunts. They like dudes, but now they are old spinsters and they live together. When Thelma breaks her hip, a civil union gives Louise power of attorney, no mess, no fuss.
I imagine a system where common-law marriage is a civil union. And since anyone can get them, 'marriage' becomes nothing more than a label thrown on top. It doesn't mean a damn thing, except that you had an entirely unnecessary ceremony. Of course, the justices and priests have a right to refuse to perform a homosexual marriage. But they are also completely separate from the civil union. The state grants the union, there is no ceremony. They go find a justice who performs homosexual ceremonies, and they have one, and they are married.
Just remember that what makes you married isn't taking a vow, or the words on a piece of paper, or the attitude the law has for you. I know a lesbian couple. The state says they aren't married, that they can't marry. But they are most definitely a married couple, and anyone who met them would agree.