You're not really checking in, you are preregistering. You are taking care of some of the paperwork before you arrive. So one possible advantage is that the check in process once you arrive should be quicker because your packet will be printed up already.
Another possible advantage is that during online check in, you inform them what time you expect to arrive. If you are arriving prior to official check in time, 3PM, and you don't have any room requests you have a better chance of your room being ready upon arrival.