I was intrigued to learn this because I have conflicting feelings on the matter. This has always been a feature in this series, but this is the first time that I've ever been tempted to use it myself. I find myself tempted because it saves a ton of time and, in most cases, the computer gets better results than I would. However,I've thought about it and I think that using QC/not using QC effectively splits HoMM 6 into different two games. One of them is an exploring/strategy game with pictures of creatures that "fight" for you so you can accomplish a given task. The other is an exploring/strategy game wherein you gather armies with unique strengths and weaknesses and lead them into battle, making sure to use each in the most efficient way possible in order to accomplish a given task. Which one sounds more exciting to you?
One could argue that, even when taking part in combat, the units are just little models that wave their arms around. They are no more alive than a static picture. Despite that, the models certainly feel more real. Watching them go forth and beat the crap out of bad guys is much more engaging and emotional than just watching the numbers go up and down. Beyond that, there is an incredible amount of suspense and thrill that comes of out of a close match that simply doesn't occur on the QC aftermath panel.
In the end, it's a trade-off. Both are good choices in my opinion. My plan from here is to only use QC when I'm already familiar with the units/fights and do it manually when I've got new guys to try out or it's a special fight. And, as mentioned, there's always the choice to go back and do each fight yourself should you choose. Game on!
P.S. I bet Ubisoft's online forums have a huge discussion on this issue, but their forums are down for "maintenance" and have been for the past week.