Well, the long format is the "real" format of eventing. Events are scheduled in particular order for a reason, and one of the main principles of the event is that a horse needs to stay fit and sound after the cross-country effort, and that it needs to be able to come back the next day and carefully jump over delicate obstacles. Jumping becomes more challenging after going all-out on the cross-country, as horses tend to lose their shape over the obstacles.
Short formats (and other formats, like the combined format) are used as stepping stones, or for a training, on the way to the ultimate goal of eventing... For example, next year pretty much everyone who is going to Tokyo will enter a short format a couple of weeks before, just as a final preparation.