A lot of people pointed out that you statement is far from the rule, but i will explain it to you anyway.
You are right that a lot of third installments aren't liked the best. Why is simple. They are the ending and the ending is IMPORTANT. A lot of times things are set up as a trilogie and the third installment is supposed to be the peak, the best. Since it's mostly not it gets a lot of dislike, even if it's allright.
That's the very same reason i have to dismiss a lot of the examples for good third installments people are giving, because most of the good ones are just third installments and not the third act of something.
Far Cry 3, has hardly anything to do with the other two storywise, as does morrowind and other examples.
One very good example for an amazing third part is return of the kings, of course, but also A Storm of Swords (Third book of a Song of Ice and Fire (Game of Thrones)). And i think i kinda get what makes each part good.
The First one has to set the scene and get things rolling.
The second one has to keep things going, up the stakes a bit, keep people excited.
The Third one has do stuff. It has to up the stakes drastically, make stuff happen and generally just be epic.