Pro's: flexibility, variety, used correctly stronger.
Cons: subject to contamination and faster wear.
Pro's: longer life under typical under-vehicle conditions especially offroading.
Con's: limited configurations and range of movement, generally weaker especially under certain stresses.
Misalignment spacers allow the Heim ball to rotate a greater range inside the cage (or vice-versa, lol). Imagine in the shot from my track bar below, that the bracket was bolted up right up against the side of the ball.
Those spacers on either side of the ball in this case do two things. The cage can rotate with greater freedom around the ball without hitting the bracket, and also here they reduce the 5/8" hole to 1/2" for my bolt.
There is another type of spacer called a cone spacer. It is simply a thick washer that is flat on one side, and beveled or "coned" on the other side. You use these typically when stacking heims say on a spindle arm where the drag link and tie rod join the spindle using one bolt. I'll find a pic of that for you and one of a cone spacer.
They are also used on link arms for 4-links and so forth.