I believe neither is better. It's a matter of taste. The"C" transformer favors the vintage side of things a little more and is brighter. The "A" is darker and a little more modern. I have an "A" and have no desire to try the "C". I know Metalhead had a "C" transformer and ordered another one after he sold the amp with the 'C" and prefers the "A" also. Johnyjellybean prefers the "A" also. I am sure the "C" kicks ass as well.
I agree with everything glip22 just said. I've had modern classics with both transformers. The C's were tighter and brighter and the A's were a little thicker. Both were great. Personally, I liked the MC with the C's a little bit better.