I was always hesitant to do online check in, I go twice a year. At WL I've never experienced any lines at check in.
But this year I decided to give it a try.
At AKL, last August, we did say we planned on arriving at 9:00 am, but room wasn't ready. That was ok, I didn't expect it to be. Resort was at full capacity or close to. So no magical upgrades, but I did get all my room requests!
So in January, I decided to try it again. Our room was ready early, and once again I got all my requests. Couldn't have asked for a better room location

.
So I wouldn't hesitate about using online check in again. One note, when I do on line check in, I will take the room assigned. Asking for a different room isn't what on line check in is geared for. Look at it as the express lane. It's set up to take your packet and go.
I have heard of people doing on line check in, and still getting free upgrades. I don't know if doing on line check in increases or decreases your chances of getting pixie dust?
I think when they finally roll out the new system with Fast Pass + it will mean if you want that, and personalized Magic Bands, you will have to do online check in. It's going to be a game changer.