Pro
Your credit card will be on file and the CM will not have to scan and verify it so saves time.
Your KTTW cards are already made up. And you should get the complete
DVC packet, including perks, map of resort, schedule of activities, the permit for your car (most of this is already together and ready to go).
If the resort has a manned separated Online check in line, you can skip the regular line. The Online check in is usually quicker because the KTTW is printed and your CC is on file.
It really helps to have online check in if you happen to arrive right after a
DCL or ME bus arrives or if you happen to be on one of the buses.
BTW, we've used online checkin three times and never have gotten into our room before 2:30 PM.
Con
Your room is already assigned and if you want a different one it will cause a delay.
Sometimes people have multiple requests for a room. E.g. At BLT, a high floor on the north, and the room number is an even number. Often the CM that assigns a room will just look at the first item on the request list. However, you might think the third item is more important, so you what a different room.
Some of the resorts do not have an online check in line or often do not have it manned. So you don't save any time waiting in line.
If you wish to use a Disney Visa Rewards Card or gift card for part of your account expenses you can't use online check in. The resort will automatically charge your account to the CC on file for online check in. I understand you can get it fixed but it takes longer than if you hadn't provided a CC to begin with.