Lines can be long for check in and 20 minutes later be gone, sort of like the park lines. Depends on how many ME busses come in from the airport, if it's a busier than usual check in day, convention people arriving at the resort (some large ones have a separate check in area, but most don't), etc. Early morning or dinnertime might be best, but the desks are not fully staffed during those times either. Around lunchtime the lines can get long as those with early a.m. flights begin to arrive.
We've noticed that when larger crowds are expected many more front desk stations are staffed, and that the guest services desk directly opposite the front desk will also handle check ins. So even if lines look long people checking in don't wait an exceptionaly long time.