The most locations that ever appeared was six (6) and the animations are sped up or slowed down depending on the number shown.
A grid was made for each location that appeared in each episode, here.
There were three main rules explained by producer Greg Spence;
First, as a rule, every episode's map must contain King's Landing, Winterfell, The Wall, and "wherever Daenerys is at the moment" - even if Daenerys does not appear in that episode.
Second, they don't always have the time and resources to create specific animations for every minor location - thus the capital of a region is often used as a stand-in to represent the overall territory.
Third, and perhaps most importantly, they can only show a limited number of locations in the 90 second duration of the opening sequence.