If you have room requests that will make or break your trip, such as having your rooms close together, then you shouldn't do online check in. You should check in at the front desk where they can discuss the available inventory with you and you can decide on rooms that fit your needs.
I seldom make room requests, so online check in works well for me. I've used it for every stay but one since they started offering it. I would have used it for the one - but it was for BLT on opening day and they didn't let anyone do online check in for that day. I have received good locations and views for my stays and I doubt if I've spent five minutes between arriving at the resort and heading for my room.