My thoughts are this; for highs and lows I only advanced-counter when my opponent is being super-predictable, or in situations that happen a lot. Like Rikuto said, the beginning of a match is a pretty good time to do it.
Also, Tina, Genfu, and Hitomi all love 1P. They don't love it so much after they get tossed like a rag doll across the stage.
And of course, nothing is better than destroying half a life bar off a 50/50 guess with a high-counter, advanced low kick hold on wake up.
For mids, its different. In theory, since you have to guess between kick or punch anyways, you should always add an extra input for a lot more damage. But in the heat of battle in can be difficult, especially on reaction counters, to add the extra input for the advanced counters.
Since early in 4 when I realized Lei and Bayman had advanced counters, I always try to practice doing advanced mid counters, but I only remember to do it like half the time.