We decide based on several factors.
One factor that we always consider is weather. We feel MK is the best park in the rain as the attractions are densely packed and it is very easy to see and do a lot without getting soaked. A park like EC, on the other hand, has a small number of pavillions that are a good distance from each other so you'll get drenched going from one to the next.
We won't do AK on the 1st or 2nd day of our trip. That park is much more laid back and relaxing. We prefer to save it for mid-trip after a couple of hectic days in the other parks. Its a great place to slow down, enjoy the surroundings and clear your head from the hustle and bustle of MK, EC or MGM. Also, AK closes earlier so it makes for a shorter day of park time. We'll usually spend that evening hotel-hopping or doing something offsite.
Lots of things to consider. Ultimately, there is no right or wrong way to do it. Just remember to take your time and have fun!