I've found that it is really important to listen to my body during STS, and also to FEED it properly! I'm eating about 200 calories more on average during the day, from the extra muscle and the extra effort in the workouts. Without that extra nutrition, I'd be exhausted. My bodyfat percentage is dropping - so I know the extra calories are not going into fat
Also, I vary the intensity of my cardio. Some days a brisk hike is plenty. I also have lower key exercises, like Kari Anderson's Reach, that let me gently move my body and get the kinks worked out. I'll use those on the days that my arms and legs feel like big lead blocks.
Sometimes, too, I'll start the cardio a bit lower key and then work up to a higher level of intensity. Ilaria's powerstrike series is a good example of a workout that makes this easy. Also, if I'm doing HIIT with Cardio Coach or IMAX, I'll use something else for fifteen or twenty minutes to loosen up. Usually that's enough.
Really, though, I personally feel far worse when I don't work out at least half an hour on the day after an STS disk; my muscles stiffen up on the day after, and then they *really* feel stiff and sore on day 2. With the cardio to loosen things up, that doesn't happen.