There is no real advantage. The only potential advantage is faster check-in. Let me try to explain the pro's and con's as best I can.
1. If you have specific requirements, online check-in may not be good. The reason is your rooms are assigned and your package is complete. You cannot make changes in the online check-in line. You will need to go to the regular check-in line after to have those changes remedied. (waiting in line twice, they do not put you to the front of the other line)
2. If you are not familiar with the resort or WDW in general, online check-in is not much benefit. The CMs are not supposed to walk you through everything that is offered, details of the resort, where the buses are, where the food court is, and anything like that. It is more for Disney veterans that do not need the attention.
3. If you want to check-in quicker (potentially) without being given the exceptional details from the CM, online check-in is great. You go up, hand them a license, they verify the reservation, grab a package, and you are on your way. It can be done in a matter of minutes depending on the lines.
4. Check-in in general: For some reason, it can be hilarious to watch. There are 3 CMs working online check-in with 2 people in line. Then there are 2 CMs working regular check-in with 10 people in line. I think a Kiosk systems at the resort for online check-in would be better, but that is my opinion.
I have done both and they are both good. We had a situation with PC where we required 1st floor rooms. We did online check-in, listed it as a medical necessity, paid for preferred, and were given 3rd floor rooms as far away as possible. They wanted us to lug all our stuff back, wait in line at the lobby again to see if there was anything they could do. It was not acceptable and I was not getting off the phone with them until it was resolved. It took another hour to be corrected as Bell Service was waiting there with our luggage. If we had not done online check-in, we would not have had an issue.
Don't get me wrong, the CMs were apologetic, courteous, and exceptional as always. However, their mistake wasted nearly 2 hours of our time to correct their mistake.