I favor the Canonet. In fact, the reason I sold my one and only Yashica were, precisely:
-Size. Too big for me; I was used to the Canonet's easy-to-handle size, features and everything.
-Automation. While both can be "automatic", the Yashica is more so. With the Canonet, should you run out of juice, you still have a perfect manual, meterless camera. With the Yashica... your tough luck.
-Batteries. Easier to get for the Canonet. If you buy a Yashica, make sure to get one with the Yashica-guy battery adapter. The original batteries for the camera are discontinued, and you can use the LR-44 (or some such kind) with a small adapter.
-Metering. The Canonet meters as close as TTL as it can be done; the meter window is right above the front element of the lens, and if you put a protective filter on it, you also protect the meter window. The Yashica meters from a window next to the RF, and it's extremely easy to block it without noticing. By the same token, it's also easy to make the mistake of shooting with the lens cap on (I did it).
Pros of the Yashica:
-Filters. The lens takes 55mm filters, as opposed to the hard-to-find 48mm for the Canonet.
-Splendid meter. While I never compared them, the Yashica meter is very reliable.
-Ease of use. If it weren't for the focusing, the Yashica would be a vintage point-and-shoot.
There you go... Again, I'm going to recommend the Canonet, but at least I do it after explainign the good, the bad and the ugly about them.