Practially speaking, opening up marriage is just so much easier. All of the laws that apply to heterosexual couples will automatically be applied to homosexual couples, and all the centuries of precedent that protect those laws. All this requires is writing a law that says, in effect, "Marriage can be between people of the same gender," and you're pretty much done.
Civil unions, on the other hand, would require creating a duplicate law for every right, priviledge, and protection currently conveyed by marriage. And you can bet that passing each and every one of those individual laws is going to be a titanic struggle, and there's no way we're going to win all of them. Plus, there's no precedent to the new laws. They're open to all sorts of lawsuits challenging them, suits that have long since been settled in regards to marriage. The whole process is insanely complicated, massively expensive, ridiculously drawn out, and the end result still won't be total equity.
And then there's the principle of the thing, which is that changing the laws to recognize gay marriage as identical, in rights and in terminology, to straight marriage is a powerful message of acceptance and tolerance. Civil unions would single gays out as a group that for some reason requires seperate legislation. Even if its for something as trivial as what you call the governmental recognition of an intimate relationship, gays are set aside as legally different from everyone else, and I think that's kinda scary. Calling it marriage erases any legal differences between gays and straights. We're all just citizens, with exactly the same rights and responsibilities, free to hate each other for whatever fucked up reason we care to come up with, but equal in the eyes of our government.