I find there's pros and cons for both the SNES and PC versions of Ultima VI, so it's difficult for me to side with one or the other. One of the pros of the SNES version is you see more of the world at any given time when wandering around, as opposed to the PC version where your view is much more limited in comparison.
No, I don't think it uses the Super NES Mouse. And I don't think that when it was brought over to North America that the programmers would have wanted to redesign everything to accommodate the mouse, if that was ever a thought that cropped up in their minds. The Japanese port came out a few months before the mouse did in Japan (although the game came out in April of 1992, the in-game credits say 1991 for some reason), so that's probably one solid reason for there being no mouse support in the North American version.
Personally, I never really found the controls to be all that bad. It certainly is different compared with the original PC version, but the way it was restructured I find still works fairly well.
No problem! And there's more to come!